Pathway Analysis for MOFA (Top 5% features per factor)
John Zhuang
2024-06-17
library(multiMiR)## Welcome to multiMiR.
##
## multiMiR database URL has been set to the
## default value: http://multimir.org/
##
## Database Version: 2.3.0 Updated: 2020-04-15library(clusterProfiler)## ## clusterProfiler v4.12.2 Learn more at https://yulab-smu.top/contribution-knowledge-mining/
##
## Please cite:
##
## S Xu, E Hu, Y Cai, Z Xie, X Luo, L Zhan, W Tang, Q Wang, B Liu, R Wang,
## W Xie, T Wu, L Xie, G Yu. Using clusterProfiler to characterize
## multiomics data. Nature Protocols. 2024, doi:10.1038/s41596-024-01020-z##
## Attaching package: 'clusterProfiler'## The following object is masked from 'package:multiMiR':
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## select## The following object is masked from 'package:stats':
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## filterlibrary(org.Hs.eg.db)## Loading required package: AnnotationDbi## Loading required package: stats4## Loading required package: BiocGenerics##
## Attaching package: 'BiocGenerics'## The following objects are masked from 'package:stats':
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## IQR, mad, sd, var, xtabs## The following objects are masked from 'package:base':
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## anyDuplicated, aperm, append, as.data.frame, basename, cbind,
## colnames, dirname, do.call, duplicated, eval, evalq, Filter, Find,
## get, grep, grepl, intersect, is.unsorted, lapply, Map, mapply,
## match, mget, order, paste, pmax, pmax.int, pmin, pmin.int,
## Position, rank, rbind, Reduce, rownames, sapply, setdiff, table,
## tapply, union, unique, unsplit, which.max, which.min## Loading required package: Biobase## Welcome to Bioconductor
##
## Vignettes contain introductory material; view with
## 'browseVignettes()'. To cite Bioconductor, see
## 'citation("Biobase")', and for packages 'citation("pkgname")'.## Loading required package: IRanges## Loading required package: S4Vectors##
## Attaching package: 'S4Vectors'## The following object is masked from 'package:clusterProfiler':
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## rename## The following object is masked from 'package:utils':
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## findMatches## The following objects are masked from 'package:base':
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## expand.grid, I, unname##
## Attaching package: 'IRanges'## The following object is masked from 'package:clusterProfiler':
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## slice## The following object is masked from 'package:grDevices':
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## windows##
## Attaching package: 'AnnotationDbi'## The following object is masked from 'package:clusterProfiler':
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## select## library(stringr)
library(ggplot2)The results here are deprecated in favor of MOFA variables selected using thres_L.
0. Loading of Results
A. List of all Gene names in the dataset
gene.names = readRDS("data/derived/unique_gene_names.rds")B. Selected Features
results.mofa = readRDS("data/sel_features/results_mofa_top_5_percent.rds")
sel.features = results.mofa
sel.features## $`1f`
## $`1f`$Factor1
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193 hsa-mir-1197 hsa-mir-136
## -0.7629508 -0.7462546 -0.6264293 -0.8177493 -0.6225595
## hsa-mir-154 hsa-mir-323 hsa-mir-323b hsa-mir-329-1 hsa-mir-329-2
## -0.6243017 -0.7085735 -0.7171871 -0.9023781 -0.6506600
## hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-377 hsa-mir-380
## -0.6299468 -0.6462057 -0.7213440 -0.6137607 -0.7333177
## hsa-mir-382 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-431
## -0.6338445 -0.6219059 -0.6434716 -0.6958073 -0.6248299
## hsa-mir-432 hsa-mir-433 hsa-mir-485 hsa-mir-487a hsa-mir-487b
## -0.6426433 -0.6436876 -0.6906152 -0.7452065 -0.6615326
## hsa-mir-494 hsa-mir-496 hsa-mir-539 hsa-mir-541 hsa-mir-543
## -0.6393844 -0.6347435 -0.6248115 -0.6876863 -0.6419155
## hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-770
## -0.7051487 -0.7722097 -0.6770739 -0.8606763 -0.7888620
## hsa-mir-889
## -0.6473752
##
##
## $`2f`
## $`2f`$Factor1
## hsa-mir-1258 hsa-mir-135b hsa-mir-506 hsa-mir-507 hsa-mir-508
## -0.2733195 0.2678525 -0.3185482 -0.2603344 -0.2774065
## hsa-mir-509-1 hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1
## -0.2576410 -0.2573185 -0.2687342 -0.3650144 -0.3297462
## hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2
## -0.3227300 -0.3234853 -0.2877525 -0.3280582 -0.3258505
## hsa-mir-514-3 hsa-mir-605 STMN1.R2Gn CTNNA1.R2Gn G6PD.RPPA
## -0.3244563 -0.2620651 0.2568932 -0.2694667 -0.4501249
## IGFBP2.RPPA RBM15.RPPA ATM.RPPA BRCA2.RPPA FASN.RPPA
## 0.3018783 0.7999696 0.3250985 -0.2550553 1.0536463
## INPP4B.RPPA TSC1.RPPA TTF1.RPPA VHL.RPPA PRDX1.RPPA
## -0.4189671 0.4269544 -0.3765308 -0.5905985 -0.5384414
## XBP1.RPPA GAPDH.RPPA MSH6.RPPA TFRC.RPPA MSH2.RPPA
## -0.3626753 0.2545084 0.7180545 0.4532162 0.2702868
## PREX1.RPPA
## -0.4629907
##
## $`2f`$Factor2
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193 hsa-mir-1197 hsa-mir-127
## -0.8148004 -0.7998948 -0.6412522 -0.8151468 -0.6292322
## hsa-mir-136 hsa-mir-154 hsa-mir-323 hsa-mir-323b hsa-mir-329-1
## -0.6456195 -0.6491630 -0.7357216 -0.7650560 -0.9230492
## hsa-mir-329-2 hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-380
## -0.6390089 -0.6397646 -0.6545057 -0.7125216 -0.7394387
## hsa-mir-382 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-431
## -0.6500180 -0.6377656 -0.6699741 -0.7572727 -0.6241728
## hsa-mir-432 hsa-mir-433 hsa-mir-485 hsa-mir-487a hsa-mir-487b
## -0.6549299 -0.6954934 -0.7505666 -0.7678460 -0.6853095
## hsa-mir-494 hsa-mir-496 hsa-mir-539 hsa-mir-541 hsa-mir-543
## -0.6570549 -0.6631960 -0.6498181 -0.6976724 -0.7016385
## hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-770
## -0.7417666 -0.7694766 -0.6560661 -0.9011633 -0.7715128
## hsa-mir-889
## -0.6736458
##
##
## $`3f`
## $`3f`$Factor1
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193 hsa-mir-1197 hsa-mir-136
## -0.7649038 -0.7472290 -0.6257883 -0.8151400 -0.6246587
## hsa-mir-154 hsa-mir-323 hsa-mir-323b hsa-mir-329-1 hsa-mir-329-2
## -0.6272125 -0.7104303 -0.7207944 -0.9035395 -0.6551830
## hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-377 hsa-mir-380
## -0.6311082 -0.6467226 -0.7206759 -0.6144270 -0.7321005
## hsa-mir-382 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-431
## -0.6356706 -0.6233494 -0.6455569 -0.7016670 -0.6259743
## hsa-mir-432 hsa-mir-433 hsa-mir-485 hsa-mir-487a hsa-mir-487b
## -0.6441280 -0.6460453 -0.6992923 -0.7463014 -0.6639803
## hsa-mir-494 hsa-mir-496 hsa-mir-539 hsa-mir-541 hsa-mir-543
## -0.6413019 -0.6368647 -0.6271768 -0.6866341 -0.6493149
## hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-770
## -0.7073773 -0.7716958 -0.6887911 -0.8602373 -0.7952202
## hsa-mir-889
## -0.6500319
##
## $`3f`$Factor2
## hsa-mir-1258 hsa-mir-135b hsa-mir-139 hsa-mir-182 hsa-mir-183
## -0.4302970 0.2926786 0.3497486 0.2766422 0.2841530
## hsa-mir-196a-1 hsa-mir-196b hsa-mir-2114 hsa-mir-218-1 hsa-mir-218-2
## 0.2896094 0.2862292 -0.3140284 0.2630450 0.3165759
## hsa-mir-3166 hsa-mir-3170 hsa-mir-3655 hsa-mir-3923 hsa-mir-485
## 0.3280705 0.2912757 -0.3138855 0.2732425 -0.2914957
## hsa-mir-506 hsa-mir-507 hsa-mir-508 hsa-mir-509-1 hsa-mir-509-2
## -0.8235410 -0.8798237 -0.7841521 -0.7517999 -0.7475504
## hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1 hsa-mir-513a-2 hsa-mir-513b
## -0.7555578 -0.9424875 -0.8275008 -0.9246400 -0.7336730
## hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2 hsa-mir-514-3 hsa-mir-514b
## -0.7541221 -0.8465889 -0.8511083 -0.8518621 -0.7302340
## hsa-mir-543 hsa-mir-615 hsa-mir-887 RBM15.RPPA TSC1.RPPA
## -0.2690902 0.2833678 0.2814917 0.3592209 0.3981680
## VHL.RPPA
## -0.4164379
##
## $`3f`$Factor3
## ERBB3.R2Gn EIF4EBP1.R2Gn RAD51.R2Gn GATA3.R2Gn EIF4G1.R2Gn
## 0.1783920 -0.1062276 -0.1104642 -0.1367058 0.2075635
## BIRC2.R2Gn XRCC5.R2Gn ADAR.R2Gn BRCA2.R2Gn CDH3.R2Gn
## 0.1173165 0.1651795 0.1023714 -0.1202103 -0.1410888
## PDCD4.R2Gn PTK2.R2Gn PRRT2.R2Gn CDK1.R2Gn MS4A1.R2Gn
## 0.1247360 0.1060514 -0.1404151 -0.1130961 -0.1204415
## LCK.R2Gn CTNNA1.R2Gn AR.R2Gn TP63.R2Gn GAPDH.R2Gn
## -0.1014332 0.1033851 -0.1052590 -0.1298156 -0.1045300
## CCNB1.R2Gn KRT5.R2Gn MYH9.R2Gn FOXM1.R2Gn YWHAB.R2Gn
## -0.1019111 -0.1134706 0.1640659 -0.1226586 0.1995448
## EZH2.R2Gn RAB25.R2Gn TFRC.R2Gn CCNE2.R2Gn ERRFI1.R2Gn
## -0.1077541 -0.1242253 0.1097051 -0.1034474 0.1602822
## PARP1.R2Gn NAPSA.R2Gn TFF1.R2Gn MACC1.R2Gn CHGA.R2Gn
## 0.1888216 -0.1226086 -0.1282434 -0.1100881 -0.1047388
## KCNJ13.R2Gn
## -0.1289491
##
##
## $`5f`
## $`5f`$Factor1
## hsa-mir-101-2 hsa-mir-146a hsa-mir-150 hsa-mir-362 FASN.R2Gn
## -0.1386771 -0.1437377 -0.1506117 -0.1510695 0.1568808
## PRKCA.R2Gn ANLN.R2Gn STMN1.R2Gn CDK1.R2Gn CTNNA1.R2Gn
## -0.1520284 0.1453249 0.1986635 0.2107954 -0.1736660
## TYMS.R2Gn CCNB1.R2Gn FOXM1.R2Gn YWHAB.R2Gn G6PD.RPPA
## 0.1766839 0.1914999 0.1679303 -0.1412905 -0.2784869
## IGFBP2.RPPA RBM15.RPPA GATA3.RPPA ATM.RPPA BRCA2.RPPA
## 0.2231534 0.5884744 -0.3249034 0.2610943 -0.2230770
## FASN.RPPA INPP4B.RPPA ACVRL1.RPPA TSC1.RPPA TTF1.RPPA
## 0.9309107 -0.3657546 -0.1384248 0.2800193 -0.2885557
## CDK1.RPPA IRS1.RPPA VHL.RPPA PRDX1.RPPA XBP1.RPPA
## -0.2259187 -0.1483742 -0.4192049 -0.4660874 -0.3349707
## GAPDH.RPPA MSH6.RPPA MYH11.RPPA TFRC.RPPA MSH2.RPPA
## 0.3190805 0.6825490 -0.2656290 0.4747938 0.2681282
## PREX1.RPPA
## -0.3944828
##
## $`5f`$Factor2
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193 hsa-mir-1197 hsa-mir-127
## -0.7585875 -0.7579153 -0.6106161 -0.8063115 -0.6067963
## hsa-mir-136 hsa-mir-154 hsa-mir-323 hsa-mir-323b hsa-mir-329-1
## -0.6274709 -0.6174549 -0.7101262 -0.7288977 -0.9205374
## hsa-mir-329-2 hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-380
## -0.6773367 -0.6270633 -0.6579611 -0.6664014 -0.7120968
## hsa-mir-382 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-431
## -0.6251879 -0.6185533 -0.6469681 -0.6913067 -0.6398707
## hsa-mir-432 hsa-mir-433 hsa-mir-485 hsa-mir-487a hsa-mir-487b
## -0.6475080 -0.6672985 -0.6710682 -0.7257411 -0.6719176
## hsa-mir-494 hsa-mir-496 hsa-mir-539 hsa-mir-541 hsa-mir-543
## -0.6089900 -0.6448792 -0.6358414 -0.6879424 -0.6286093
## hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-770
## -0.6985868 -0.7680615 -0.7129604 -0.8759764 -0.8024955
## hsa-mir-889
## -0.6434183
##
## $`5f`$Factor3
## hsa-mir-1185-1 hsa-mir-1258 hsa-mir-135b hsa-mir-139 hsa-mir-182
## -0.2693898 -0.3686553 0.2490502 0.3217925 0.2398068
## hsa-mir-183 hsa-mir-196b hsa-mir-2114 hsa-mir-218-2 hsa-mir-3166
## 0.2430847 0.2401641 -0.2789480 0.2598653 0.2902097
## hsa-mir-3170 hsa-mir-3655 hsa-mir-376a-2 hsa-mir-3923 hsa-mir-411
## 0.2486504 -0.2836783 -0.2643668 0.2339307 -0.2921805
## hsa-mir-485 hsa-mir-487a hsa-mir-494 hsa-mir-506 hsa-mir-507
## -0.3417393 -0.2342592 -0.2366182 -0.7359853 -0.8076562
## hsa-mir-508 hsa-mir-509-1 hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510
## -0.7308223 -0.7148668 -0.7105480 -0.7097014 -0.8157004
## hsa-mir-513a-1 hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c hsa-mir-514-1
## -0.7257079 -0.8095509 -0.6391351 -0.6802698 -0.7502505
## hsa-mir-514-2 hsa-mir-514-3 hsa-mir-514b hsa-mir-543 hsa-mir-615
## -0.7560365 -0.7577167 -0.6915826 -0.3114163 0.2358871
## hsa-mir-668
## -0.2524937
##
## $`5f`$Factor4
## hsa-mir-100 hsa-mir-10a hsa-mir-1226 hsa-mir-1249 hsa-mir-1258
## 0.09092840 0.10430926 -0.09205737 0.09425247 -0.08713839
## hsa-mir-133b hsa-mir-136 hsa-mir-139 hsa-mir-195 hsa-mir-27a
## 0.08922739 0.09398186 0.11903941 0.12217991 0.08887515
## hsa-mir-29c hsa-mir-301a hsa-mir-3200 hsa-mir-338 hsa-mir-421
## 0.11238619 -0.09142878 -0.11185583 0.08631410 -0.08392455
## hsa-mir-424 hsa-mir-431 hsa-mir-450a-1 hsa-mir-450a-2 hsa-mir-483
## 0.10314917 -0.09069324 0.09329516 0.09112324 -0.15440452
## hsa-mir-497 hsa-mir-518c hsa-mir-937 hsa-mir-940 hsa-mir-95
## 0.10858906 0.10784148 -0.08603576 -0.09177980 0.10658063
## G6PD.RPPA PTEN.RPPA PEA15.RPPA EGFR.RPPA FASN.RPPA
## -0.14609040 0.09169299 0.19406851 0.12075721 0.08668146
## CDK1.RPPA IRS1.RPPA VHL.RPPA XBP1.RPPA MSH2.RPPA
## -0.09550971 0.09575202 -0.11997307 -0.12221368 -0.09643250
## PREX1.RPPA
## -0.13058908
##
## $`5f`$Factor5
## MAPK14.R2Gn ERBB3.R2Gn AKT2.R2Gn RAD51.R2Gn GATA3.R2Gn EIF4G1.R2Gn
## 0.10707272 0.15159766 0.10220584 -0.08782818 -0.10681824 0.17254253
## MAPK1.R2Gn BIRC2.R2Gn XRCC5.R2Gn BRCA2.R2Gn LCN2.R2Gn CDH3.R2Gn
## 0.09778135 0.12000357 0.16537122 -0.10494009 -0.09685022 -0.13429995
## PDCD4.R2Gn PTK2.R2Gn PRRT2.R2Gn MS4A1.R2Gn LCK.R2Gn AR.R2Gn
## 0.10885774 0.10031383 -0.13514514 -0.11782608 -0.10713095 -0.11004834
## TP63.R2Gn GAPDH.R2Gn NRG1.R2Gn KRT5.R2Gn MYH9.R2Gn FOXM1.R2Gn
## -0.11901601 -0.08857987 -0.09126953 -0.10776611 0.14014417 -0.09110170
## YWHAB.R2Gn RAB25.R2Gn ERCC1.R2Gn BID.R2Gn TFRC.R2Gn ERRFI1.R2Gn
## 0.16302468 -0.11733783 -0.08760359 -0.09582430 0.10668702 0.13746126
## PARP1.R2Gn NAPSA.R2Gn TFF1.R2Gn MACC1.R2Gn CHGA.R2Gn KCNJ13.R2Gn
## 0.18604508 -0.11670010 -0.11688121 -0.11090805 -0.09129306 -0.12196921
##
##
## $`10f`
## $`10f`$Factor1
## hsa-mir-146a hsa-mir-150 hsa-mir-196a-1 hsa-mir-362 hsa-mir-653
## 0.2439511 0.2176340 -0.1894599 0.2013512 0.2167146
## FASN.R2Gn PRKCA.R2Gn STMN1.R2Gn CDK1.R2Gn CTNNA1.R2Gn
## -0.1960203 0.1897229 -0.2373242 -0.2289052 0.2068288
## TYMS.R2Gn MSH6.R2Gn CCNB1.R2Gn PREX1.R2Gn G6PD.RPPA
## -0.1729913 -0.1780294 -0.2314913 0.1735357 0.4649610
## IGFBP2.RPPA ASNS.RPPA RBM15.RPPA GATA3.RPPA PEA15.RPPA
## -0.2495660 0.1845150 -0.7031606 0.4185162 -0.1961371
## ATM.RPPA BRCA2.RPPA FASN.RPPA INPP4B.RPPA TSC1.RPPA
## -0.2976696 0.2778099 -1.1854465 0.4445420 -0.3088216
## TTF1.RPPA CDK1.RPPA VHL.RPPA PRDX1.RPPA XBP1.RPPA
## 0.3018635 0.3171725 0.5434133 0.5653009 0.3994834
## GAPDH.RPPA MSH6.RPPA MYH11.RPPA TFRC.RPPA MSH2.RPPA
## -0.5204806 -0.8080000 0.2798145 -0.4650862 -0.2984680
## PREX1.RPPA
## 0.5079902
##
## $`10f`$Factor2
## hsa-mir-1185-1 hsa-mir-1185-2 hsa-mir-1193 hsa-mir-1197 hsa-mir-127
## -0.7757787 -0.7684686 -0.6118972 -0.8106640 -0.6143032
## hsa-mir-136 hsa-mir-154 hsa-mir-323 hsa-mir-323b hsa-mir-329-1
## -0.6320459 -0.6310229 -0.7222756 -0.7419769 -0.9263064
## hsa-mir-329-2 hsa-mir-370 hsa-mir-376a-1 hsa-mir-376a-2 hsa-mir-380
## -0.6799496 -0.6314871 -0.6638160 -0.6738463 -0.7232468
## hsa-mir-382 hsa-mir-409 hsa-mir-410 hsa-mir-411 hsa-mir-431
## -0.6325155 -0.6230285 -0.6622328 -0.7261397 -0.6425268
## hsa-mir-432 hsa-mir-433 hsa-mir-485 hsa-mir-487a hsa-mir-487b
## -0.6511705 -0.6874613 -0.6997358 -0.7420009 -0.6732689
## hsa-mir-494 hsa-mir-496 hsa-mir-539 hsa-mir-541 hsa-mir-543
## -0.6323493 -0.6429590 -0.6406990 -0.6928630 -0.6504994
## hsa-mir-655 hsa-mir-656 hsa-mir-665 hsa-mir-668 hsa-mir-770
## -0.7303706 -0.7603929 -0.6939368 -0.8925683 -0.7861210
## hsa-mir-889
## -0.6554383
##
## $`10f`$Factor3
## hsa-let-7a-1 hsa-let-7a-2 hsa-let-7a-3 hsa-let-7f-1 hsa-let-7f-2 hsa-mir-1229
## -0.05801089 -0.05686941 -0.05791394 -0.06823632 -0.06271406 0.06294886
## hsa-mir-214 hsa-mir-23a hsa-mir-3200 G6PD.RPPA IGFBP2.RPPA RBM15.RPPA
## -0.05434345 -0.05925805 0.05633602 0.35292467 0.22359502 -0.30910647
## PTEN.RPPA GATA3.RPPA PEA15.RPPA ATM.RPPA BRCA2.RPPA EGFR.RPPA
## -0.45634142 0.14007989 -0.22443563 -0.25097775 0.11915235 -0.15185097
## FASN.RPPA INPP4B.RPPA PCNA.RPPA ACVRL1.RPPA TSC1.RPPA PDCD4.RPPA
## 0.08621731 0.20455523 0.09210050 0.14015430 -0.18266179 -0.41097477
## CDK1.RPPA XRCC1.RPPA IRS1.RPPA VHL.RPPA AR.RPPA PRDX1.RPPA
## 0.16809660 0.08300330 -0.12852126 0.22653894 -0.07744230 0.25950259
## XBP1.RPPA NF2.RPPA ERCC1.RPPA TFRC.RPPA MSH2.RPPA PREX1.RPPA
## 0.24001938 -0.10919836 -0.14765766 -0.17888249 0.12918670 0.21356429
##
## $`10f`$Factor4
## hsa-mir-1226 hsa-mir-1249 hsa-mir-1258 hsa-mir-135b hsa-mir-139
## 0.2013880 0.2013092 -0.3447852 0.2185706 0.2925311
## hsa-mir-182 hsa-mir-183 hsa-mir-184 hsa-mir-196b hsa-mir-2114
## 0.2095041 0.2128228 -0.2045339 0.2097269 -0.2516953
## hsa-mir-218-2 hsa-mir-3166 hsa-mir-3170 hsa-mir-3655 hsa-mir-376a-2
## 0.2043498 0.2622004 0.2178932 -0.2656059 -0.2118430
## hsa-mir-3923 hsa-mir-485 hsa-mir-506 hsa-mir-507 hsa-mir-508
## 0.2342099 -0.2529788 -0.6782678 -0.7587051 -0.6876708
## hsa-mir-509-1 hsa-mir-509-2 hsa-mir-509-3 hsa-mir-510 hsa-mir-513a-1
## -0.6887159 -0.6844518 -0.6827294 -0.8044964 -0.6867524
## hsa-mir-513a-2 hsa-mir-513b hsa-mir-513c hsa-mir-514-1 hsa-mir-514-2
## -0.7446260 -0.6228126 -0.6547784 -0.6779802 -0.6837980
## hsa-mir-514-3 hsa-mir-514b hsa-mir-543 hsa-mir-582 hsa-mir-615
## -0.6835320 -0.6983735 -0.2354951 0.2105771 0.2115752
## hsa-mir-92b
## 0.2082682
##
## $`10f`$Factor5
## hsa-mir-1224 hsa-mir-125a hsa-mir-202 hsa-mir-29c hsa-mir-301a
## -0.07757617 -0.07368264 -0.07087204 -0.09390491 0.07492819
## hsa-mir-766 EIF4EBP1.R2Gn NRAS.R2Gn MAPK9.R2Gn EGFR.R2Gn
## -0.08679421 0.06772254 0.07322794 -0.10262868 -0.08042480
## ACVRL1.R2Gn PECAM1.R2Gn RAB11A.R2Gn EEF2K.R2Gn RAD50.R2Gn
## 0.07327735 0.07790451 -0.10008703 -0.09475668 -0.11121136
## TYMS.R2Gn XIAP.R2Gn PARP1.R2Gn ANXA7.R2Gn IGFBP2.RPPA
## 0.07976948 -0.07202139 0.08127678 -0.08679935 0.14329337
## ASNS.RPPA RBM15.RPPA PTEN.RPPA ATM.RPPA BRCA2.RPPA
## 0.12955621 0.14449525 -0.12278367 0.09622584 0.06847188
## EGFR.RPPA ACVRL1.RPPA TSC1.RPPA TTF1.RPPA CDK1.RPPA
## -0.17544550 0.08678960 0.15464054 -0.07050533 0.07800888
## IRS1.RPPA GAPDH.RPPA MSH6.RPPA PDK1.RPPA ERCC1.RPPA
## -0.06691432 -0.16643153 0.08321948 -0.06834891 -0.19305989
## TFRC.RPPA
## 0.07729538
##
## $`10f`$Factor6
## AKT1S1.R2Gn SRC.R2Gn MAPK1.R2Gn VASP.R2Gn ITGA2.R2Gn YWHAE.R2Gn
## -0.06530473 -0.06137238 0.07006741 -0.07346763 0.06533720 -0.09718410
## TSC1.R2Gn ANLN.R2Gn PDCD4.R2Gn GSK3A.R2Gn RAB11B.R2Gn KEAP1.R2Gn
## -0.06199414 0.08852450 -0.06254116 -0.08128472 -0.07358222 -0.06263774
## XRCC1.R2Gn PDK1.R2Gn MAP2K1.R2Gn FOXM1.R2Gn ERCC1.R2Gn G6PD.RPPA
## -0.10397790 0.06057473 0.09030174 0.07717057 -0.07147568 0.14335443
## ASNS.RPPA RBM15.RPPA PTEN.RPPA GATA3.RPPA PEA15.RPPA ATM.RPPA
## 0.19428484 -0.28288889 -0.06120672 -0.18584156 0.13874172 -0.11923894
## EGFR.RPPA PDCD4.RPPA IRS1.RPPA VHL.RPPA XBP1.RPPA GAPDH.RPPA
## 0.16687511 -0.08123798 0.12930401 -0.06729201 -0.09220541 0.16526712
## MSH6.RPPA MYH11.RPPA NF2.RPPA PDK1.RPPA TFRC.RPPA PREX1.RPPA
## 0.07068952 -0.13618457 -0.11466402 0.06047169 0.09673942 -0.20894785
##
## $`10f`$Factor7
## hsa-mir-3074 MAPK14.R2Gn ERBB3.R2Gn AKT3.R2Gn CDH2.R2Gn RAD51.R2Gn
## 0.07930424 -0.09080391 -0.09733605 -0.07428569 -0.08697511 0.07849700
## BECN1.R2Gn BIRC2.R2Gn ITGA2.R2Gn ADAR.R2Gn BRCA2.R2Gn PCNA.R2Gn
## -0.09878736 -0.06614775 -0.07324430 -0.12430753 0.06620272 0.12726545
## CTNNB1.R2Gn ANLN.R2Gn SHC1.R2Gn STMN1.R2Gn ACACB.R2Gn CDK1.R2Gn
## -0.07196339 0.22669883 -0.09211306 0.22997268 -0.07505351 0.20357363
## E2F1.R2Gn XRCC1.R2Gn TYMS.R2Gn CCNB1.R2Gn TUBA1B.R2Gn NOTCH3.R2Gn
## 0.11854476 0.07422303 0.13062122 0.21480298 0.10910680 0.07228020
## FOXM1.R2Gn EZH2.R2Gn CCNE2.R2Gn ERRFI1.R2Gn PARP1.R2Gn RPTOR.R2Gn
## 0.18389165 0.10342199 0.09657363 -0.08004816 -0.10325056 -0.07926491
## CDKN2A.R2Gn PEA15.RPPA INPP4B.RPPA PCNA.RPPA ACVRL1.RPPA NF2.RPPA
## 0.09057715 -0.06904783 -0.06605250 0.07415823 -0.06682102 -0.07900642
##
## $`10f`$Factor8
## ERBB3.R2Gn EIF4EBP1.R2Gn AKT2.R2Gn CLDN7.R2Gn ESR1.R2Gn
## -0.08224300 0.07072022 -0.08641771 0.08638426 0.07944772
## GATA3.R2Gn EIF4G1.R2Gn AXL.R2Gn MAPK1.R2Gn BIRC2.R2Gn
## 0.07285401 -0.13453801 0.07267915 -0.08100040 -0.07640026
## XRCC5.R2Gn LCN2.R2Gn CDH3.R2Gn PDCD4.R2Gn PTK2.R2Gn
## -0.11221777 0.07404122 0.10597123 -0.08704497 -0.07893465
## PRRT2.R2Gn MS4A1.R2Gn LCK.R2Gn CTNNA1.R2Gn TP63.R2Gn
## 0.09576759 0.09444701 0.09407651 -0.07267374 0.09729126
## NRG1.R2Gn KRT5.R2Gn MYH9.R2Gn YWHAB.R2Gn RAB25.R2Gn
## 0.07899287 0.09340290 -0.08806494 -0.13172348 0.09895545
## BID.R2Gn TFRC.R2Gn ERRFI1.R2Gn PARP1.R2Gn CASP9.R2Gn
## 0.08035962 -0.08377423 -0.07313473 -0.11041104 0.07580432
## NAPSA.R2Gn SYK.R2Gn TFF1.R2Gn MACC1.R2Gn CHGA.R2Gn
## 0.09265782 0.09534506 0.09923044 0.08408040 0.08330778
## KCNJ13.R2Gn
## 0.09958442
##
## $`10f`$Factor9
## hsa-let-7a-1 hsa-let-7a-3 hsa-let-7e hsa-let-7f-1 hsa-let-7f-2
## -0.07351197 -0.07362586 -0.10535952 -0.09033088 -0.09345894
## hsa-mir-10a hsa-mir-1197 hsa-mir-1249 hsa-mir-128-2 hsa-mir-134
## 0.08653057 -0.07932135 0.07170332 -0.07785700 0.07713903
## hsa-mir-142 hsa-mir-146b hsa-mir-195 hsa-mir-197 hsa-mir-205
## 0.11448278 0.07687828 0.08075973 0.07460224 0.09066726
## hsa-mir-2110 hsa-mir-29c hsa-mir-3200 hsa-mir-421 hsa-mir-483
## -0.08394032 0.07649425 -0.08255380 -0.10029192 -0.10543139
## hsa-mir-514b hsa-mir-516a-1 hsa-mir-516a-2 hsa-mir-516b-1 hsa-mir-517a
## 0.09014382 0.08803593 0.09923389 0.08826557 0.10131671
## hsa-mir-518b hsa-mir-518c hsa-mir-518f hsa-mir-519a-2 hsa-mir-525
## 0.09169916 0.10279340 0.11103735 0.08638884 0.07590113
## hsa-mir-526b hsa-mir-627 hsa-mir-655 hsa-mir-765 hsa-mir-877
## 0.07759569 0.09695566 0.08207855 -0.09110382 -0.08039207
## hsa-mir-98
## -0.07509896
##
## $`10f`$Factor10
## hsa-mir-106a hsa-mir-107 hsa-mir-10b hsa-mir-1226 hsa-mir-125a
## 0.08792105 0.05218595 -0.05511979 -0.06467026 -0.05393226
## hsa-mir-125b-1 hsa-mir-1307 hsa-mir-144 hsa-mir-16-1 hsa-mir-16-2
## -0.04745908 -0.04976137 0.06520889 0.05097669 0.04599367
## hsa-mir-185 hsa-mir-18a hsa-mir-19a hsa-mir-19b-2 hsa-mir-20a
## 0.05757672 0.08705410 0.04928057 0.05379727 0.05476943
## hsa-mir-20b hsa-mir-223 hsa-mir-23a hsa-mir-301a hsa-mir-30e
## 0.05628907 0.05646559 -0.06209031 -0.05890957 -0.05636798
## hsa-mir-328 hsa-mir-363 hsa-mir-374b hsa-mir-377 hsa-mir-451
## -0.05122608 0.09423997 0.05124469 0.04763857 0.06474881
## hsa-mir-486 hsa-mir-510 hsa-mir-550a-1 hsa-mir-616 hsa-mir-652
## 0.05457522 0.04980592 0.06231136 -0.04829336 0.05510786
## hsa-mir-660 hsa-mir-99b BRCA2.RPPA PCNA.RPPA IRS1.RPPA
## 0.04716566 -0.08297141 0.06675472 0.05366337 0.09403171
## NF2.RPPA
## 0.069432421. Convert microRNA to genes
Also remove the ending “.R2Gn” and “.RPPA” from gene names.
split.by.omic = function(variable.list) {
out.mRSG = variable.list[startsWith(variable.list, "hsa")]
out.R2Gn = variable.list[endsWith(variable.list, ".R2Gn")]
out.RPPA = variable.list[endsWith(variable.list, ".RPPA")]
out = list("miRNASeqGene" = out.mRSG,
"RNASeq2GeneNorm" = out.R2Gn,
"RPPAArray" = out.RPPA)
out
}multiomics.to.GENES = function(sel.features, full.search = F, table = "validated", drop.miRNA = F) {
multiomics.list = split.by.omic(sel.features)
# Convert miRNASeqGene to target GENE names
# Skipped and returns an empty list instead of the list of select features,
# or if microRNA features are explicitly dropped (drop.miRNA = T).
# (Usually done when the features has only a few miRNA and unable to target any genes)
if (length(multiomics.list[[1]]) > 0 & !drop.miRNA) {
if (!full.search) { # Search only among the 198 genes in ACC, recommended
targets= get_multimir(mirna = multiomics.list[[1]],
target = gene.names,
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
} else { # Search the full dataset, not recommended.
# Use only if ACC gene search returns nothing or fails.
# Genes not in the ACC genes need to be manually removed.
targets= get_multimir(mirna = multiomics.list[[1]],
table = table,
summary = T)
mRSG.target.genes = unique(targets@data$target_symbol)
}
} else {
mRSG.target.genes = list()
}
#Remove suffix for Pathway Analysis Compatibility
R2Gn.genes = str_remove(multiomics.list[[2]], ".R2Gn")
RPPA.genes = str_remove(multiomics.list[[3]], ".RPPA")
#Join all cleaned-up genes are remove duplicates.
out1 = c(mRSG.target.genes, R2Gn.genes, RPPA.genes)
out = as.character(unique(out1))
out
}geneNames <- list("Factor1of1"= multiomics.to.GENES(names(sel.features$`1f`$Factor1)),
"Factor1of2"= multiomics.to.GENES(names(sel.features$`2f`$Factor1)),
"Factor2of2"= multiomics.to.GENES(names(sel.features$`2f`$Factor2)),
"Factor1of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor1)),
"Factor2of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor2)),
"Factor3of3"= multiomics.to.GENES(names(sel.features$`3f`$Factor3)),
"Factor1of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor1), drop.miRNA = T),
"Factor2of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor2)),
"Factor3of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor3)),
"Factor4of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor4)),
"Factor5of5"= multiomics.to.GENES(names(sel.features$`5f`$Factor5)),
"Factor1of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor1), drop.miRNA = T),
"Factor2of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor2)),
"Factor3of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor3), drop.miRNA = T),
"Factor4of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor4)),
"Factor5of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor5), drop.miRNA = T),
"Factor6of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor6)),
"Factor7of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor7), drop.miRNA = T),
"Factor8of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor8)),
"Factor9of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor9)),
"Factor10of10"= multiomics.to.GENES(names(sel.features$`10f`$Factor10))
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## Searching tarbase ...geneNames## $Factor1of1
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A" "FOXO3"
## [9] "ATM" "CASP8" "MACC1" "PTEN" "KRAS" "NRAS" "PTK2" "ETS1"
## [17] "CCND1" "XIAP" "STAT5A" "YAP1" "ITGA2" "MAPK1" "ANLN"
##
## $Factor1of2
## [1] "RB1" "XIAP" "ETS1" "MAPK8" "ARID1A" "BID" "NCOA3" "GAB2"
## [9] "STMN1" "CTNNA1" "G6PD" "IGFBP2" "RBM15" "ATM" "BRCA2" "FASN"
## [17] "INPP4B" "TSC1" "TTF1" "VHL" "PRDX1" "XBP1" "GAPDH" "MSH6"
## [25] "TFRC" "MSH2" "PREX1"
##
## $Factor2of2
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A" "FOXO3"
## [9] "ATM" "CASP8" "MACC1" "PTEN" "KRAS" "NRAS" "PTK2" "ETS1"
## [17] "CCND1" "XIAP" "STAT5A" "YAP1" "ITGA2" "MAPK1" "ANLN"
##
## $Factor1of3
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A" "FOXO3"
## [9] "ATM" "CASP8" "MACC1" "PTEN" "KRAS" "NRAS" "PTK2" "ETS1"
## [17] "CCND1" "XIAP" "STAT5A" "YAP1" "ITGA2" "MAPK1" "ANLN"
##
## $Factor2of3
## [1] "RB1" "XIAP" "ETS1" "MAPK8" "ARID1A" "BID" "PTEN" "KRAS"
## [9] "NRAS" "PTK2" "ATM" "YWHAZ" "CCND1" "CDKN1A" "NCOA3" "GAB2"
## [17] "ITGA2" "RBM15" "TSC1" "VHL"
##
## $Factor3of3
## [1] "ERBB3" "EIF4EBP1" "RAD51" "GATA3" "EIF4G1" "BIRC2"
## [7] "XRCC5" "ADAR" "BRCA2" "CDH3" "PDCD4" "PTK2"
## [13] "PRRT2" "CDK1" "MS4A1" "LCK" "CTNNA1" "AR"
## [19] "TP63" "GAPDH" "CCNB1" "KRT5" "MYH9" "FOXM1"
## [25] "YWHAB" "EZH2" "RAB25" "TFRC" "CCNE2" "ERRFI1"
## [31] "PARP1" "NAPSA" "TFF1" "MACC1" "CHGA" "KCNJ13"
##
## $Factor1of5
## [1] "FASN" "PRKCA" "ANLN" "STMN1" "CDK1" "CTNNA1" "TYMS" "CCNB1"
## [9] "FOXM1" "YWHAB" "G6PD" "IGFBP2" "RBM15" "GATA3" "ATM" "BRCA2"
## [17] "INPP4B" "ACVRL1" "TSC1" "TTF1" "IRS1" "VHL" "PRDX1" "XBP1"
## [25] "GAPDH" "MSH6" "MYH11" "TFRC" "MSH2" "PREX1"
##
## $Factor2of5
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A" "FOXO3"
## [9] "ATM" "CASP8" "MACC1" "PTEN" "KRAS" "NRAS" "PTK2" "ETS1"
## [17] "CCND1" "XIAP" "STAT5A" "YAP1" "ITGA2" "MAPK1" "ANLN"
##
## $Factor3of5
## [1] "RB1" "XIAP" "ETS1" "MAPK8" "ARID1A" "BID" "PTEN" "KRAS"
## [9] "NRAS" "PTK2" "ATM" "YWHAZ" "CCND1" "CDKN1A" "NCOA3" "ITGA2"
## [17] "GAB2"
##
## $Factor4of5
## [1] "EGFR" "MET" "AKT1" "BCL2L1" "IGF1R" "CASP3"
## [7] "CDH1" "ATM" "XIAP" "SMAD4" "MAPK8" "TUBA1B"
## [13] "RB1" "NF2" "E2F1" "MYH9" "MYC" "YWHAZ"
## [19] "CASP8" "RAD51" "NDRG1" "ACVRL1" "NCOA3" "PARP1"
## [25] "EIF4EBP1" "NRAS" "CDKN1B" "CTNNA1" "MTOR" "PRDX1"
## [31] "SERPINE1" "PRKAA1" "PXN" "SRSF1" "TFRC" "YWHAB"
## [37] "ERBB2" "ADAR" "JUN" "NOTCH3" "BCL2L11" "TP53"
## [43] "AKT2" "XBP1" "STAT3" "EEF2" "EIF4G1" "GAPDH"
## [49] "VASP" "ARID1A" "AKT1S1" "RICTOR" "PTCH1" "FASN"
## [55] "G6PD" "PTEN" "PEA15" "CDK1" "IRS1" "VHL"
## [61] "MSH2" "PREX1"
##
## $Factor5of5
## [1] "MAPK14" "ERBB3" "AKT2" "RAD51" "GATA3" "EIF4G1" "MAPK1" "BIRC2"
## [9] "XRCC5" "BRCA2" "LCN2" "CDH3" "PDCD4" "PTK2" "PRRT2" "MS4A1"
## [17] "LCK" "AR" "TP63" "GAPDH" "NRG1" "KRT5" "MYH9" "FOXM1"
## [25] "YWHAB" "RAB25" "ERCC1" "BID" "TFRC" "ERRFI1" "PARP1" "NAPSA"
## [33] "TFF1" "MACC1" "CHGA" "KCNJ13"
##
## $Factor1of10
## [1] "FASN" "PRKCA" "STMN1" "CDK1" "CTNNA1" "TYMS" "MSH6" "CCNB1"
## [9] "PREX1" "G6PD" "IGFBP2" "ASNS" "RBM15" "GATA3" "PEA15" "ATM"
## [17] "BRCA2" "INPP4B" "TSC1" "TTF1" "VHL" "PRDX1" "XBP1" "GAPDH"
## [25] "MYH11" "TFRC" "MSH2"
##
## $Factor2of10
## [1] "HSPA1A" "AKT1" "VHL" "MTOR" "MAPK8" "MYH9" "CDKN1A" "FOXO3"
## [9] "ATM" "CASP8" "MACC1" "PTEN" "KRAS" "NRAS" "PTK2" "ETS1"
## [17] "CCND1" "XIAP" "STAT5A" "YAP1" "ITGA2" "MAPK1" "ANLN"
##
## $Factor3of10
## [1] "G6PD" "IGFBP2" "RBM15" "PTEN" "GATA3" "PEA15" "ATM" "BRCA2"
## [9] "EGFR" "FASN" "INPP4B" "PCNA" "ACVRL1" "TSC1" "PDCD4" "CDK1"
## [17] "XRCC1" "IRS1" "VHL" "AR" "PRDX1" "XBP1" "NF2" "ERCC1"
## [25] "TFRC" "MSH2" "PREX1"
##
## $Factor4of10
## [1] "AKT2" "BCL2" "MYC" "AKT1" "BCL2L1" "RB1" "XIAP" "ETS1"
## [9] "MAPK8" "ARID1A" "BID" "PTEN" "KRAS" "NRAS" "PTK2" "ATM"
## [17] "YWHAZ" "CCND1" "CDKN1A" "NCOA3" "ITGA2" "GAB2"
##
## $Factor5of10
## [1] "EIF4EBP1" "NRAS" "MAPK9" "EGFR" "ACVRL1" "PECAM1"
## [7] "RAB11A" "EEF2K" "RAD50" "TYMS" "XIAP" "PARP1"
## [13] "ANXA7" "IGFBP2" "ASNS" "RBM15" "PTEN" "ATM"
## [19] "BRCA2" "TSC1" "TTF1" "CDK1" "IRS1" "GAPDH"
## [25] "MSH6" "PDK1" "ERCC1" "TFRC"
##
## $Factor6of10
## [1] "AKT1S1" "SRC" "MAPK1" "VASP" "ITGA2" "YWHAE" "TSC1" "ANLN"
## [9] "PDCD4" "GSK3A" "RAB11B" "KEAP1" "XRCC1" "PDK1" "MAP2K1" "FOXM1"
## [17] "ERCC1" "G6PD" "ASNS" "RBM15" "PTEN" "GATA3" "PEA15" "ATM"
## [25] "EGFR" "IRS1" "VHL" "XBP1" "GAPDH" "MSH6" "MYH11" "NF2"
## [33] "TFRC" "PREX1"
##
## $Factor7of10
## [1] "MAPK14" "ERBB3" "AKT3" "CDH2" "RAD51" "BECN1" "BIRC2" "ITGA2"
## [9] "ADAR" "BRCA2" "PCNA" "CTNNB1" "ANLN" "SHC1" "STMN1" "ACACB"
## [17] "CDK1" "E2F1" "XRCC1" "TYMS" "CCNB1" "TUBA1B" "NOTCH3" "FOXM1"
## [25] "EZH2" "CCNE2" "ERRFI1" "PARP1" "RPTOR" "CDKN2A" "PEA15" "INPP4B"
## [33] "ACVRL1" "NF2"
##
## $Factor8of10
## [1] "ERBB3" "EIF4EBP1" "AKT2" "CLDN7" "ESR1" "GATA3"
## [7] "EIF4G1" "AXL" "MAPK1" "BIRC2" "XRCC5" "LCN2"
## [13] "CDH3" "PDCD4" "PTK2" "PRRT2" "MS4A1" "LCK"
## [19] "CTNNA1" "TP63" "NRG1" "KRT5" "MYH9" "YWHAB"
## [25] "RAB25" "BID" "TFRC" "ERRFI1" "PARP1" "CASP9"
## [31] "NAPSA" "SYK" "TFF1" "MACC1" "CHGA" "KCNJ13"
##
## $Factor9of10
## [1] "CASP3" "CDH1" "ATM" "XIAP" "SMAD4" "MAPK8"
## [7] "TUBA1B" "YWHAZ" "EIF4G1" "YWHAE" "ARID1A" "NDRG1"
## [13] "INPP4B" "TP53" "AR" "MAPK1" "FASN" "CDKN1A"
## [19] "STAT5A" "NF2" "NRAS" "ADAR" "PREX1" "MYH9"
## [25] "CCND1" "CDKN1B" "BCL2L11" "PARP1" "ANXA7" "CTNNA1"
## [31] "EEF2" "MTOR" "GSK3B" "IGF1R" "PRDX1" "SERPINE1"
## [37] "PRKAA1" "PXN" "SRSF1" "SYP" "TFRC" "WWTR1"
## [43] "YWHAB" "MACC1"
##
## $Factor10of10
## [1] "CCNE1" "PTEN" "CAV1" "PIK3R1" "CDK1" "IDH3A"
## [7] "ITGA2" "RAD51" "RPS6KB1" "SRSF1" "PEA15" "TUBA1B"
## [13] "CHGA" "MAPK14" "E2F1" "NRAS" "ADAR" "MYH9"
## [19] "CCND1" "CDKN1A" "IRS1" "MYC" "EGFR" "TP63"
## [25] "ARAF" "JUN" "MSH2" "EZH2" "MAPK9" "PIK3R2"
## [31] "BRCA2" "PTGS2" "TYMS" "TP53" "AKT2" "MAP2K1"
## [37] "NFKB1" "ERRFI1" "AKT3" "BIRC2" "CCNB1" "CTNNA1"
## [43] "CTNNB1" "EEF2" "EIF4G1" "FOXM1" "GSK3B" "IGF1R"
## [49] "IGFBP2" "SMAD4" "SERPINE1" "PCNA" "PRKAA1" "PRKCA"
## [55] "MAPK3" "MAPK8" "PXN" "TFRC" "TGM2" "ARID1A"
## [61] "BECN1" "RAB11A" "SQSTM1" "ANLN" "INPP4B" "YWHAB"
## [67] "FASN" "RAB11B" "BRAF" "PRRT2" "MACC1" "NF2"saveRDS(geneNames, file = "data/sel_features/gene_converted/genes_mofa_top_5_percent.rds")2. Pathway Analysis
A. GO Classification
ggo_MF <- list()#functional profile of a geneset for Molecular Function
ggo_BP <- list()#functional profile of a geneset for Biological Process
ggo_CC <- list()#functional profile of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ggo_MF[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="MF",
keyType="SYMBOL",
readable=TRUE)
ggo_BP[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="BP",
keyType="SYMBOL",
readable=TRUE)
ggo_CC[[z]] <- groupGO(gene=input,
OrgDb = org.Hs.eg.db,
ont="CC",
keyType="SYMBOL",
readable=TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## [1] 20
## [1] 21for(z in 1:length(geneNames)) {
print(head(ggo_MF[[z]]))
print(head(ggo_BP[[z]]))
print(head(ggo_CC[[z]]))
}## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/23
## GO:0003824 GO:0003824 catalytic activity 15 15/23
## GO:0005198 GO:0005198 structural molecule activity 0 0/23
## GO:0005215 GO:0005215 transporter activity 0 0/23
## GO:0005488 GO:0005488 binding 23 23/23
## GO:0009055 GO:0009055 electron transfer activity 0 0/23
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/XIAP/MAPK1
## GO:0005198
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/23
## GO:0002376 GO:0002376 immune system process 14 14/23
## GO:0008152 GO:0008152 metabolic process 21 21/23
## GO:0009987 GO:0009987 cellular process 23 23/23
## GO:0016032 GO:0016032 viral process 3 3/23
## GO:0022414 GO:0022414 reproductive process 8 8/23
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/XIAP/ITGA2/MAPK1
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0016032 HSPA1A/AKT1/ITGA2
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 13 13/23
## GO:0044423 GO:0044423 virion component 0 0/23
## GO:0110165 GO:0110165 cellular anatomical entity 23 23/23
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/STAT5A/YAP1/ITGA2
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/27
## GO:0003824 GO:0003824 catalytic activity 13 13/27
## GO:0005198 GO:0005198 structural molecule activity 1 1/27
## GO:0005215 GO:0005215 transporter activity 0 0/27
## GO:0005488 GO:0005488 binding 27 27/27
## GO:0009055 GO:0009055 electron transfer activity 0 0/27
## geneID
## GO:0003774
## GO:0003824 XIAP/MAPK8/NCOA3/G6PD/ATM/BRCA2/FASN/INPP4B/VHL/PRDX1/GAPDH/MSH6/MSH2
## GO:0005198 CTNNA1
## GO:0005215
## GO:0005488 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/NCOA3/GAB2/STMN1/CTNNA1/G6PD/IGFBP2/RBM15/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 7 7/27
## GO:0002376 GO:0002376 immune system process 19 19/27
## GO:0008152 GO:0008152 metabolic process 23 23/27
## GO:0009987 GO:0009987 cellular process 27 27/27
## GO:0016032 GO:0016032 viral process 1 1/27
## GO:0022414 GO:0022414 reproductive process 7 7/27
## geneID
## GO:0000003 RB1/CTNNA1/IGFBP2/ATM/BRCA2/MSH6/MSH2
## GO:0002376 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/GAB2/G6PD/IGFBP2/RBM15/ATM/TSC1/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0008152 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/NCOA3/G6PD/RBM15/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0009987 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/NCOA3/GAB2/STMN1/CTNNA1/G6PD/IGFBP2/RBM15/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0016032 TFRC
## GO:0022414 RB1/CTNNA1/IGFBP2/ATM/BRCA2/MSH6/MSH2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 14 14/27
## GO:0044423 GO:0044423 virion component 0 0/27
## GO:0110165 GO:0110165 cellular anatomical entity 27 27/27
## geneID
## GO:0032991 RB1/ETS1/ARID1A/NCOA3/CTNNA1/RBM15/ATM/BRCA2/TSC1/XBP1/GAPDH/MSH6/TFRC/MSH2
## GO:0044423
## GO:0110165 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/NCOA3/GAB2/STMN1/CTNNA1/G6PD/IGFBP2/RBM15/ATM/BRCA2/FASN/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/23
## GO:0003824 GO:0003824 catalytic activity 15 15/23
## GO:0005198 GO:0005198 structural molecule activity 0 0/23
## GO:0005215 GO:0005215 transporter activity 0 0/23
## GO:0005488 GO:0005488 binding 23 23/23
## GO:0009055 GO:0009055 electron transfer activity 0 0/23
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/XIAP/MAPK1
## GO:0005198
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/23
## GO:0002376 GO:0002376 immune system process 14 14/23
## GO:0008152 GO:0008152 metabolic process 21 21/23
## GO:0009987 GO:0009987 cellular process 23 23/23
## GO:0016032 GO:0016032 viral process 3 3/23
## GO:0022414 GO:0022414 reproductive process 8 8/23
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/XIAP/ITGA2/MAPK1
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0016032 HSPA1A/AKT1/ITGA2
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 13 13/23
## GO:0044423 GO:0044423 virion component 0 0/23
## GO:0110165 GO:0110165 cellular anatomical entity 23 23/23
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/STAT5A/YAP1/ITGA2
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/23
## GO:0003824 GO:0003824 catalytic activity 15 15/23
## GO:0005198 GO:0005198 structural molecule activity 0 0/23
## GO:0005215 GO:0005215 transporter activity 0 0/23
## GO:0005488 GO:0005488 binding 23 23/23
## GO:0009055 GO:0009055 electron transfer activity 0 0/23
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/XIAP/MAPK1
## GO:0005198
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/23
## GO:0002376 GO:0002376 immune system process 14 14/23
## GO:0008152 GO:0008152 metabolic process 21 21/23
## GO:0009987 GO:0009987 cellular process 23 23/23
## GO:0016032 GO:0016032 viral process 3 3/23
## GO:0022414 GO:0022414 reproductive process 8 8/23
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/XIAP/ITGA2/MAPK1
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0016032 HSPA1A/AKT1/ITGA2
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 13 13/23
## GO:0044423 GO:0044423 virion component 0 0/23
## GO:0110165 GO:0110165 cellular anatomical entity 23 23/23
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/STAT5A/YAP1/ITGA2
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/20
## GO:0003824 GO:0003824 catalytic activity 11 11/20
## GO:0005198 GO:0005198 structural molecule activity 0 0/20
## GO:0005215 GO:0005215 transporter activity 0 0/20
## GO:0005488 GO:0005488 binding 20 20/20
## GO:0009055 GO:0009055 electron transfer activity 0 0/20
## geneID
## GO:0003774
## GO:0003824 XIAP/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CCND1/CDKN1A/NCOA3/VHL
## GO:0005198
## GO:0005215
## GO:0005488 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/GAB2/ITGA2/RBM15/TSC1/VHL
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 4 4/20
## GO:0002376 GO:0002376 immune system process 14 14/20
## GO:0008152 GO:0008152 metabolic process 18 18/20
## GO:0009987 GO:0009987 cellular process 20 20/20
## GO:0016032 GO:0016032 viral process 1 1/20
## GO:0022414 GO:0022414 reproductive process 4 4/20
## geneID
## GO:0000003 RB1/PTEN/ATM/ITGA2
## GO:0002376 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/CDKN1A/GAB2/ITGA2/RBM15/TSC1
## GO:0008152 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/RBM15/TSC1/VHL
## GO:0009987 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/GAB2/ITGA2/RBM15/TSC1/VHL
## GO:0016032 ITGA2
## GO:0022414 RB1/PTEN/ATM/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 10 10/20
## GO:0044423 GO:0044423 virion component 0 0/20
## GO:0110165 GO:0110165 cellular anatomical entity 20 20/20
## geneID
## GO:0032991 RB1/ETS1/ARID1A/ATM/CCND1/CDKN1A/NCOA3/ITGA2/RBM15/TSC1
## GO:0044423
## GO:0110165 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/GAB2/ITGA2/RBM15/TSC1/VHL
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/36
## GO:0003824 GO:0003824 catalytic activity 13 13/36
## GO:0005198 GO:0005198 structural molecule activity 2 2/36
## GO:0005215 GO:0005215 transporter activity 1 1/36
## GO:0005488 GO:0005488 binding 34 34/36
## GO:0009055 GO:0009055 electron transfer activity 0 0/36
## geneID
## GO:0003774 MYH9
## GO:0003824 RAD51/BIRC2/XRCC5/ADAR/BRCA2/PTK2/CDK1/LCK/GAPDH/EZH2/RAB25/PARP1/NAPSA
## GO:0005198 CTNNA1/KRT5
## GO:0005215 KCNJ13
## GO:0005488 ERBB3/EIF4EBP1/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/ADAR/BRCA2/CDH3/PDCD4/PTK2/PRRT2/CDK1/MS4A1/LCK/CTNNA1/AR/TP63/GAPDH/CCNB1/KRT5/MYH9/FOXM1/YWHAB/EZH2/RAB25/TFRC/CCNE2/ERRFI1/PARP1/NAPSA/TFF1/MACC1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 11 11/36
## GO:0002376 GO:0002376 immune system process 13 13/36
## GO:0008152 GO:0008152 metabolic process 29 29/36
## GO:0009987 GO:0009987 cellular process 35 35/36
## GO:0016032 GO:0016032 viral process 3 3/36
## GO:0022414 GO:0022414 reproductive process 11 11/36
## geneID
## GO:0000003 RAD51/GATA3/BRCA2/CDK1/CTNNA1/AR/TP63/MYH9/CCNE2/ERRFI1/PARP1
## GO:0002376 GATA3/BIRC2/XRCC5/ADAR/PTK2/MS4A1/LCK/GAPDH/MYH9/EZH2/TFRC/PARP1/CHGA
## GO:0008152 ERBB3/EIF4EBP1/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/ADAR/BRCA2/CDH3/PDCD4/PTK2/CDK1/LCK/AR/TP63/GAPDH/CCNB1/MYH9/FOXM1/YWHAB/EZH2/TFRC/CCNE2/ERRFI1/PARP1/NAPSA/TFF1/MACC1
## GO:0009987 ERBB3/EIF4EBP1/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/ADAR/BRCA2/CDH3/PDCD4/PTK2/PRRT2/CDK1/MS4A1/LCK/CTNNA1/AR/TP63/GAPDH/CCNB1/KRT5/MYH9/FOXM1/YWHAB/EZH2/RAB25/TFRC/CCNE2/ERRFI1/PARP1/TFF1/MACC1/CHGA/KCNJ13
## GO:0016032 ADAR/CDK1/TFRC
## GO:0022414 RAD51/GATA3/BRCA2/CDK1/CTNNA1/AR/TP63/MYH9/CCNE2/ERRFI1/PARP1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 22 22/36
## GO:0044423 GO:0044423 virion component 0 0/36
## GO:0110165 GO:0110165 cellular anatomical entity 36 36/36
## geneID
## GO:0032991 ERBB3/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/ADAR/BRCA2/CDH3/CDK1/CTNNA1/AR/TP63/GAPDH/CCNB1/MYH9/FOXM1/EZH2/TFRC/CCNE2/PARP1/KCNJ13
## GO:0044423
## GO:0110165 ERBB3/EIF4EBP1/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/ADAR/BRCA2/CDH3/PDCD4/PTK2/PRRT2/CDK1/MS4A1/LCK/CTNNA1/AR/TP63/GAPDH/CCNB1/KRT5/MYH9/FOXM1/YWHAB/EZH2/RAB25/TFRC/CCNE2/ERRFI1/PARP1/NAPSA/TFF1/MACC1/CHGA/KCNJ13
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/30
## GO:0003824 GO:0003824 catalytic activity 14 14/30
## GO:0005198 GO:0005198 structural molecule activity 2 2/30
## GO:0005215 GO:0005215 transporter activity 0 0/30
## GO:0005488 GO:0005488 binding 30 30/30
## GO:0009055 GO:0009055 electron transfer activity 0 0/30
## geneID
## GO:0003774 MYH11
## GO:0003824 FASN/PRKCA/CDK1/TYMS/G6PD/ATM/BRCA2/INPP4B/ACVRL1/VHL/PRDX1/GAPDH/MSH6/MSH2
## GO:0005198 CTNNA1/MYH11
## GO:0005215
## GO:0005488 FASN/PRKCA/ANLN/STMN1/CDK1/CTNNA1/TYMS/CCNB1/FOXM1/YWHAB/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/IRS1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/30
## GO:0002376 GO:0002376 immune system process 14 14/30
## GO:0008152 GO:0008152 metabolic process 25 25/30
## GO:0009987 GO:0009987 cellular process 30 30/30
## GO:0016032 GO:0016032 viral process 2 2/30
## GO:0022414 GO:0022414 reproductive process 8 8/30
## geneID
## GO:0000003 CDK1/CTNNA1/IGFBP2/GATA3/ATM/BRCA2/MSH6/MSH2
## GO:0002376 PRKCA/G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0008152 FASN/PRKCA/CDK1/TYMS/CCNB1/FOXM1/YWHAB/G6PD/RBM15/GATA3/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/IRS1/VHL/PRDX1/XBP1/GAPDH/MSH6/TFRC/MSH2/PREX1
## GO:0009987 FASN/PRKCA/ANLN/STMN1/CDK1/CTNNA1/TYMS/CCNB1/FOXM1/YWHAB/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/IRS1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
## GO:0016032 CDK1/TFRC
## GO:0022414 CDK1/CTNNA1/IGFBP2/GATA3/ATM/BRCA2/MSH6/MSH2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 18 18/30
## GO:0044423 GO:0044423 virion component 0 0/30
## GO:0110165 GO:0110165 cellular anatomical entity 30 30/30
## geneID
## GO:0032991 PRKCA/CDK1/CTNNA1/CCNB1/FOXM1/RBM15/GATA3/ATM/BRCA2/ACVRL1/TSC1/IRS1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2
## GO:0044423
## GO:0110165 FASN/PRKCA/ANLN/STMN1/CDK1/CTNNA1/TYMS/CCNB1/FOXM1/YWHAB/G6PD/IGFBP2/RBM15/GATA3/ATM/BRCA2/INPP4B/ACVRL1/TSC1/TTF1/IRS1/VHL/PRDX1/XBP1/GAPDH/MSH6/MYH11/TFRC/MSH2/PREX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/23
## GO:0003824 GO:0003824 catalytic activity 15 15/23
## GO:0005198 GO:0005198 structural molecule activity 0 0/23
## GO:0005215 GO:0005215 transporter activity 0 0/23
## GO:0005488 GO:0005488 binding 23 23/23
## GO:0009055 GO:0009055 electron transfer activity 0 0/23
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/XIAP/MAPK1
## GO:0005198
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/23
## GO:0002376 GO:0002376 immune system process 14 14/23
## GO:0008152 GO:0008152 metabolic process 21 21/23
## GO:0009987 GO:0009987 cellular process 23 23/23
## GO:0016032 GO:0016032 viral process 3 3/23
## GO:0022414 GO:0022414 reproductive process 8 8/23
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/XIAP/ITGA2/MAPK1
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0016032 HSPA1A/AKT1/ITGA2
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 13 13/23
## GO:0044423 GO:0044423 virion component 0 0/23
## GO:0110165 GO:0110165 cellular anatomical entity 23 23/23
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/STAT5A/YAP1/ITGA2
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/17
## GO:0003824 GO:0003824 catalytic activity 10 10/17
## GO:0005198 GO:0005198 structural molecule activity 0 0/17
## GO:0005215 GO:0005215 transporter activity 0 0/17
## GO:0005488 GO:0005488 binding 17 17/17
## GO:0009055 GO:0009055 electron transfer activity 0 0/17
## geneID
## GO:0003774
## GO:0003824 XIAP/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CCND1/CDKN1A/NCOA3
## GO:0005198
## GO:0005215
## GO:0005488 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 4 4/17
## GO:0002376 GO:0002376 immune system process 12 12/17
## GO:0008152 GO:0008152 metabolic process 15 15/17
## GO:0009987 GO:0009987 cellular process 17 17/17
## GO:0016032 GO:0016032 viral process 1 1/17
## GO:0022414 GO:0022414 reproductive process 4 4/17
## geneID
## GO:0000003 RB1/PTEN/ATM/ITGA2
## GO:0002376 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/CDKN1A/ITGA2/GAB2
## GO:0008152 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2
## GO:0009987 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
## GO:0016032 ITGA2
## GO:0022414 RB1/PTEN/ATM/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 8 8/17
## GO:0044423 GO:0044423 virion component 0 0/17
## GO:0110165 GO:0110165 cellular anatomical entity 17 17/17
## geneID
## GO:0032991 RB1/ETS1/ARID1A/ATM/CCND1/CDKN1A/NCOA3/ITGA2
## GO:0044423
## GO:0110165 RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/62
## GO:0003824 GO:0003824 catalytic activity 29 29/62
## GO:0005198 GO:0005198 structural molecule activity 2 2/62
## GO:0005215 GO:0005215 transporter activity 1 1/62
## GO:0005488 GO:0005488 binding 62 62/62
## GO:0009055 GO:0009055 electron transfer activity 0 0/62
## geneID
## GO:0003774 MYH9
## GO:0003824 EGFR/MET/AKT1/IGF1R/CASP3/ATM/XIAP/MAPK8/TUBA1B/CASP8/RAD51/ACVRL1/NCOA3/PARP1/NRAS/MTOR/PRDX1/PRKAA1/ERBB2/ADAR/AKT2/EEF2/GAPDH/FASN/G6PD/PTEN/CDK1/VHL/MSH2
## GO:0005198 TUBA1B/CTNNA1
## GO:0005215 IGF1R
## GO:0005488 EGFR/MET/AKT1/BCL2L1/IGF1R/CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/RB1/NF2/E2F1/MYH9/MYC/YWHAZ/CASP8/RAD51/NDRG1/ACVRL1/NCOA3/PARP1/EIF4EBP1/NRAS/CDKN1B/CTNNA1/MTOR/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/TFRC/YWHAB/ERBB2/ADAR/JUN/NOTCH3/BCL2L11/TP53/AKT2/XBP1/STAT3/EEF2/EIF4G1/GAPDH/VASP/ARID1A/AKT1S1/RICTOR/PTCH1/FASN/G6PD/PTEN/PEA15/CDK1/IRS1/VHL/MSH2/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 21 21/62
## GO:0002376 GO:0002376 immune system process 28 28/62
## GO:0008152 GO:0008152 metabolic process 53 53/62
## GO:0009987 GO:0009987 cellular process 62 62/62
## GO:0016032 GO:0016032 viral process 7 7/62
## GO:0022414 GO:0022414 reproductive process 20 20/62
## geneID
## GO:0000003 EGFR/AKT1/BCL2L1/IGF1R/CASP3/ATM/SMAD4/RB1/MYH9/CASP8/RAD51/PARP1/CDKN1B/CTNNA1/MTOR/BCL2L11/STAT3/PTCH1/PTEN/CDK1/MSH2
## GO:0002376 AKT1/IGF1R/CASP3/ATM/XIAP/MAPK8/RB1/MYH9/MYC/YWHAZ/CASP8/NDRG1/PARP1/MTOR/PRDX1/SERPINE1/TFRC/ERBB2/ADAR/BCL2L11/TP53/XBP1/STAT3/GAPDH/ARID1A/G6PD/MSH2/PREX1
## GO:0008152 EGFR/MET/AKT1/IGF1R/CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/RB1/NF2/E2F1/MYH9/MYC/YWHAZ/CASP8/RAD51/ACVRL1/NCOA3/PARP1/EIF4EBP1/CDKN1B/MTOR/PRDX1/SERPINE1/PRKAA1/SRSF1/TFRC/YWHAB/ERBB2/ADAR/JUN/NOTCH3/TP53/AKT2/XBP1/STAT3/EEF2/EIF4G1/GAPDH/ARID1A/AKT1S1/RICTOR/PTCH1/FASN/G6PD/PTEN/CDK1/IRS1/VHL/MSH2/PREX1
## GO:0009987 EGFR/MET/AKT1/BCL2L1/IGF1R/CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/RB1/NF2/E2F1/MYH9/MYC/YWHAZ/CASP8/RAD51/NDRG1/ACVRL1/NCOA3/PARP1/EIF4EBP1/NRAS/CDKN1B/CTNNA1/MTOR/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/TFRC/YWHAB/ERBB2/ADAR/JUN/NOTCH3/BCL2L11/TP53/AKT2/XBP1/STAT3/EEF2/EIF4G1/GAPDH/VASP/ARID1A/AKT1S1/RICTOR/PTCH1/FASN/G6PD/PTEN/PEA15/CDK1/IRS1/VHL/MSH2/PREX1
## GO:0016032 EGFR/AKT1/TFRC/ADAR/JUN/TP53/CDK1
## GO:0022414 EGFR/AKT1/BCL2L1/IGF1R/CASP3/ATM/SMAD4/RB1/MYH9/CASP8/RAD51/PARP1/CDKN1B/CTNNA1/MTOR/BCL2L11/PTCH1/PTEN/CDK1/MSH2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 44 44/62
## GO:0044423 GO:0044423 virion component 0 0/62
## GO:0110165 GO:0110165 cellular anatomical entity 62 62/62
## geneID
## GO:0032991 EGFR/MET/AKT1/BCL2L1/IGF1R/CASP3/CDH1/ATM/SMAD4/RB1/E2F1/MYH9/MYC/CASP8/RAD51/ACVRL1/NCOA3/PARP1/CDKN1B/CTNNA1/MTOR/SERPINE1/PRKAA1/PXN/SRSF1/TFRC/ERBB2/ADAR/JUN/NOTCH3/BCL2L11/TP53/XBP1/STAT3/EEF2/EIF4G1/GAPDH/ARID1A/AKT1S1/RICTOR/PEA15/CDK1/IRS1/MSH2
## GO:0044423
## GO:0110165 EGFR/MET/AKT1/BCL2L1/IGF1R/CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/RB1/NF2/E2F1/MYH9/MYC/YWHAZ/CASP8/RAD51/NDRG1/ACVRL1/NCOA3/PARP1/EIF4EBP1/NRAS/CDKN1B/CTNNA1/MTOR/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/TFRC/YWHAB/ERBB2/ADAR/JUN/NOTCH3/BCL2L11/TP53/AKT2/XBP1/STAT3/EEF2/EIF4G1/GAPDH/VASP/ARID1A/AKT1S1/RICTOR/PTCH1/FASN/G6PD/PTEN/PEA15/CDK1/IRS1/VHL/MSH2/PREX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/36
## GO:0003824 GO:0003824 catalytic activity 14 14/36
## GO:0005198 GO:0005198 structural molecule activity 1 1/36
## GO:0005215 GO:0005215 transporter activity 1 1/36
## GO:0005488 GO:0005488 binding 34 34/36
## GO:0009055 GO:0009055 electron transfer activity 0 0/36
## geneID
## GO:0003774 MYH9
## GO:0003824 MAPK14/AKT2/RAD51/MAPK1/BIRC2/XRCC5/BRCA2/PTK2/LCK/GAPDH/RAB25/ERCC1/PARP1/NAPSA
## GO:0005198 KRT5
## GO:0005215 KCNJ13
## GO:0005488 MAPK14/ERBB3/AKT2/RAD51/GATA3/EIF4G1/MAPK1/BIRC2/XRCC5/BRCA2/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/AR/TP63/GAPDH/NRG1/KRT5/MYH9/FOXM1/YWHAB/RAB25/ERCC1/BID/TFRC/ERRFI1/PARP1/NAPSA/TFF1/MACC1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 9 9/36
## GO:0002376 GO:0002376 immune system process 16 16/36
## GO:0008152 GO:0008152 metabolic process 30 30/36
## GO:0009987 GO:0009987 cellular process 35 35/36
## GO:0016032 GO:0016032 viral process 1 1/36
## GO:0022414 GO:0022414 reproductive process 9 9/36
## geneID
## GO:0000003 RAD51/GATA3/BRCA2/AR/TP63/MYH9/ERCC1/ERRFI1/PARP1
## GO:0002376 MAPK14/GATA3/MAPK1/BIRC2/XRCC5/LCN2/PTK2/MS4A1/LCK/GAPDH/MYH9/ERCC1/BID/TFRC/PARP1/CHGA
## GO:0008152 MAPK14/ERBB3/AKT2/RAD51/GATA3/EIF4G1/MAPK1/BIRC2/XRCC5/BRCA2/LCN2/CDH3/PDCD4/PTK2/LCK/AR/TP63/GAPDH/NRG1/MYH9/FOXM1/YWHAB/ERCC1/BID/TFRC/ERRFI1/PARP1/NAPSA/TFF1/MACC1
## GO:0009987 MAPK14/ERBB3/AKT2/RAD51/GATA3/EIF4G1/MAPK1/BIRC2/XRCC5/BRCA2/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/AR/TP63/GAPDH/NRG1/KRT5/MYH9/FOXM1/YWHAB/RAB25/ERCC1/BID/TFRC/ERRFI1/PARP1/TFF1/MACC1/CHGA/KCNJ13
## GO:0016032 TFRC
## GO:0022414 RAD51/GATA3/BRCA2/AR/TP63/MYH9/ERCC1/ERRFI1/PARP1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 17 17/36
## GO:0044423 GO:0044423 virion component 0 0/36
## GO:0110165 GO:0110165 cellular anatomical entity 36 36/36
## geneID
## GO:0032991 ERBB3/RAD51/GATA3/EIF4G1/BIRC2/XRCC5/BRCA2/CDH3/AR/TP63/GAPDH/MYH9/FOXM1/ERCC1/TFRC/PARP1/KCNJ13
## GO:0044423
## GO:0110165 MAPK14/ERBB3/AKT2/RAD51/GATA3/EIF4G1/MAPK1/BIRC2/XRCC5/BRCA2/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/AR/TP63/GAPDH/NRG1/KRT5/MYH9/FOXM1/YWHAB/RAB25/ERCC1/BID/TFRC/ERRFI1/PARP1/NAPSA/TFF1/MACC1/CHGA/KCNJ13
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/27
## GO:0003824 GO:0003824 catalytic activity 14 14/27
## GO:0005198 GO:0005198 structural molecule activity 2 2/27
## GO:0005215 GO:0005215 transporter activity 0 0/27
## GO:0005488 GO:0005488 binding 27 27/27
## GO:0009055 GO:0009055 electron transfer activity 0 0/27
## geneID
## GO:0003774 MYH11
## GO:0003824 FASN/PRKCA/CDK1/TYMS/MSH6/G6PD/ASNS/ATM/BRCA2/INPP4B/VHL/PRDX1/GAPDH/MSH2
## GO:0005198 CTNNA1/MYH11
## GO:0005215
## GO:0005488 FASN/PRKCA/STMN1/CDK1/CTNNA1/TYMS/MSH6/CCNB1/PREX1/G6PD/IGFBP2/ASNS/RBM15/GATA3/PEA15/ATM/BRCA2/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MYH11/TFRC/MSH2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/27
## GO:0002376 GO:0002376 immune system process 14 14/27
## GO:0008152 GO:0008152 metabolic process 22 22/27
## GO:0009987 GO:0009987 cellular process 27 27/27
## GO:0016032 GO:0016032 viral process 2 2/27
## GO:0022414 GO:0022414 reproductive process 8 8/27
## geneID
## GO:0000003 CDK1/CTNNA1/MSH6/IGFBP2/GATA3/ATM/BRCA2/MSH2
## GO:0002376 PRKCA/MSH6/PREX1/G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/GAPDH/TFRC/MSH2
## GO:0008152 FASN/PRKCA/CDK1/TYMS/MSH6/CCNB1/PREX1/G6PD/ASNS/RBM15/GATA3/ATM/BRCA2/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/TFRC/MSH2
## GO:0009987 FASN/PRKCA/STMN1/CDK1/CTNNA1/TYMS/MSH6/CCNB1/PREX1/G6PD/IGFBP2/ASNS/RBM15/GATA3/PEA15/ATM/BRCA2/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MYH11/TFRC/MSH2
## GO:0016032 CDK1/TFRC
## GO:0022414 CDK1/CTNNA1/MSH6/IGFBP2/GATA3/ATM/BRCA2/MSH2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 16 16/27
## GO:0044423 GO:0044423 virion component 0 0/27
## GO:0110165 GO:0110165 cellular anatomical entity 27 27/27
## geneID
## GO:0032991 PRKCA/CDK1/CTNNA1/MSH6/CCNB1/RBM15/GATA3/PEA15/ATM/BRCA2/TSC1/XBP1/GAPDH/MYH11/TFRC/MSH2
## GO:0044423
## GO:0110165 FASN/PRKCA/STMN1/CDK1/CTNNA1/TYMS/MSH6/CCNB1/PREX1/G6PD/IGFBP2/ASNS/RBM15/GATA3/PEA15/ATM/BRCA2/INPP4B/TSC1/TTF1/VHL/PRDX1/XBP1/GAPDH/MYH11/TFRC/MSH2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/23
## GO:0003824 GO:0003824 catalytic activity 15 15/23
## GO:0005198 GO:0005198 structural molecule activity 0 0/23
## GO:0005215 GO:0005215 transporter activity 0 0/23
## GO:0005488 GO:0005488 binding 23 23/23
## GO:0009055 GO:0009055 electron transfer activity 0 0/23
## geneID
## GO:0003774 MYH9
## GO:0003824 HSPA1A/AKT1/VHL/MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/KRAS/NRAS/PTK2/CCND1/XIAP/MAPK1
## GO:0005198
## GO:0005215
## GO:0005488 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/23
## GO:0002376 GO:0002376 immune system process 14 14/23
## GO:0008152 GO:0008152 metabolic process 21 21/23
## GO:0009987 GO:0009987 cellular process 23 23/23
## GO:0016032 GO:0016032 viral process 3 3/23
## GO:0022414 GO:0022414 reproductive process 8 8/23
## geneID
## GO:0000003 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## GO:0002376 HSPA1A/AKT1/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/PTK2/ETS1/XIAP/ITGA2/MAPK1
## GO:0008152 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1
## GO:0009987 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## GO:0016032 HSPA1A/AKT1/ITGA2
## GO:0022414 AKT1/MTOR/MYH9/FOXO3/ATM/CASP8/PTEN/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 13 13/23
## GO:0044423 GO:0044423 virion component 0 0/23
## GO:0110165 GO:0110165 cellular anatomical entity 23 23/23
## geneID
## GO:0032991 HSPA1A/AKT1/MTOR/MYH9/CDKN1A/FOXO3/ATM/CASP8/ETS1/CCND1/STAT5A/YAP1/ITGA2
## GO:0044423
## GO:0110165 HSPA1A/AKT1/VHL/MTOR/MAPK8/MYH9/CDKN1A/FOXO3/ATM/CASP8/MACC1/PTEN/KRAS/NRAS/PTK2/ETS1/CCND1/XIAP/STAT5A/YAP1/ITGA2/MAPK1/ANLN
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/27
## GO:0003824 GO:0003824 catalytic activity 15 15/27
## GO:0005198 GO:0005198 structural molecule activity 0 0/27
## GO:0005215 GO:0005215 transporter activity 0 0/27
## GO:0005488 GO:0005488 binding 27 27/27
## GO:0009055 GO:0009055 electron transfer activity 0 0/27
## geneID
## GO:0003774
## GO:0003824 G6PD/PTEN/ATM/BRCA2/EGFR/FASN/INPP4B/PCNA/ACVRL1/CDK1/XRCC1/VHL/PRDX1/ERCC1/MSH2
## GO:0005198
## GO:0005215
## GO:0005488 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/BRCA2/EGFR/FASN/INPP4B/PCNA/ACVRL1/TSC1/PDCD4/CDK1/XRCC1/IRS1/VHL/AR/PRDX1/XBP1/NF2/ERCC1/TFRC/MSH2/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 11 11/27
## GO:0002376 GO:0002376 immune system process 12 12/27
## GO:0008152 GO:0008152 metabolic process 25 25/27
## GO:0009987 GO:0009987 cellular process 27 27/27
## GO:0016032 GO:0016032 viral process 3 3/27
## GO:0022414 GO:0022414 reproductive process 11 11/27
## geneID
## GO:0000003 IGFBP2/PTEN/GATA3/ATM/BRCA2/EGFR/PCNA/CDK1/AR/ERCC1/MSH2
## GO:0002376 G6PD/IGFBP2/RBM15/GATA3/ATM/TSC1/PRDX1/XBP1/ERCC1/TFRC/MSH2/PREX1
## GO:0008152 G6PD/RBM15/PTEN/GATA3/ATM/BRCA2/EGFR/FASN/INPP4B/PCNA/ACVRL1/TSC1/PDCD4/CDK1/XRCC1/IRS1/VHL/AR/PRDX1/XBP1/NF2/ERCC1/TFRC/MSH2/PREX1
## GO:0009987 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/BRCA2/EGFR/FASN/INPP4B/PCNA/ACVRL1/TSC1/PDCD4/CDK1/XRCC1/IRS1/VHL/AR/PRDX1/XBP1/NF2/ERCC1/TFRC/MSH2/PREX1
## GO:0016032 EGFR/CDK1/TFRC
## GO:0022414 IGFBP2/PTEN/GATA3/ATM/BRCA2/EGFR/PCNA/CDK1/AR/ERCC1/MSH2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 17 17/27
## GO:0044423 GO:0044423 virion component 0 0/27
## GO:0110165 GO:0110165 cellular anatomical entity 27 27/27
## geneID
## GO:0032991 RBM15/GATA3/PEA15/ATM/BRCA2/EGFR/PCNA/ACVRL1/TSC1/CDK1/XRCC1/IRS1/AR/XBP1/ERCC1/TFRC/MSH2
## GO:0044423
## GO:0110165 G6PD/IGFBP2/RBM15/PTEN/GATA3/PEA15/ATM/BRCA2/EGFR/FASN/INPP4B/PCNA/ACVRL1/TSC1/PDCD4/CDK1/XRCC1/IRS1/VHL/AR/PRDX1/XBP1/NF2/ERCC1/TFRC/MSH2/PREX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/22
## GO:0003824 GO:0003824 catalytic activity 12 12/22
## GO:0005198 GO:0005198 structural molecule activity 0 0/22
## GO:0005215 GO:0005215 transporter activity 1 1/22
## GO:0005488 GO:0005488 binding 22 22/22
## GO:0009055 GO:0009055 electron transfer activity 0 0/22
## geneID
## GO:0003774
## GO:0003824 AKT2/AKT1/XIAP/MAPK8/PTEN/KRAS/NRAS/PTK2/ATM/CCND1/CDKN1A/NCOA3
## GO:0005198
## GO:0005215 BCL2
## GO:0005488 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 7 7/22
## GO:0002376 GO:0002376 immune system process 15 15/22
## GO:0008152 GO:0008152 metabolic process 19 19/22
## GO:0009987 GO:0009987 cellular process 22 22/22
## GO:0016032 GO:0016032 viral process 3 3/22
## GO:0022414 GO:0022414 reproductive process 7 7/22
## geneID
## GO:0000003 BCL2/AKT1/BCL2L1/RB1/PTEN/ATM/ITGA2
## GO:0002376 BCL2/MYC/AKT1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTK2/ATM/YWHAZ/CDKN1A/ITGA2/GAB2
## GO:0008152 AKT2/BCL2/MYC/AKT1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2
## GO:0009987 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
## GO:0016032 BCL2/AKT1/ITGA2
## GO:0022414 BCL2/AKT1/BCL2L1/RB1/PTEN/ATM/ITGA2
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 12 12/22
## GO:0044423 GO:0044423 virion component 0 0/22
## GO:0110165 GO:0110165 cellular anatomical entity 22 22/22
## geneID
## GO:0032991 BCL2/MYC/AKT1/BCL2L1/RB1/ETS1/ARID1A/ATM/CCND1/CDKN1A/NCOA3/ITGA2
## GO:0044423
## GO:0110165 AKT2/BCL2/MYC/AKT1/BCL2L1/RB1/XIAP/ETS1/MAPK8/ARID1A/BID/PTEN/KRAS/NRAS/PTK2/ATM/YWHAZ/CCND1/CDKN1A/NCOA3/ITGA2/GAB2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/28
## GO:0003824 GO:0003824 catalytic activity 19 19/28
## GO:0005198 GO:0005198 structural molecule activity 0 0/28
## GO:0005215 GO:0005215 transporter activity 0 0/28
## GO:0005488 GO:0005488 binding 28 28/28
## GO:0009055 GO:0009055 electron transfer activity 0 0/28
## geneID
## GO:0003774
## GO:0003824 NRAS/MAPK9/EGFR/ACVRL1/RAB11A/EEF2K/RAD50/TYMS/XIAP/PARP1/ASNS/PTEN/ATM/BRCA2/CDK1/GAPDH/MSH6/PDK1/ERCC1
## GO:0005198
## GO:0005215
## GO:0005488 EIF4EBP1/NRAS/MAPK9/EGFR/ACVRL1/PECAM1/RAB11A/EEF2K/RAD50/TYMS/XIAP/PARP1/ANXA7/IGFBP2/ASNS/RBM15/PTEN/ATM/BRCA2/TSC1/TTF1/CDK1/IRS1/GAPDH/MSH6/PDK1/ERCC1/TFRC
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 10 10/28
## GO:0002376 GO:0002376 immune system process 12 12/28
## GO:0008152 GO:0008152 metabolic process 25 25/28
## GO:0009987 GO:0009987 cellular process 28 28/28
## GO:0016032 GO:0016032 viral process 3 3/28
## GO:0022414 GO:0022414 reproductive process 10 10/28
## geneID
## GO:0000003 EGFR/RAD50/PARP1/IGFBP2/PTEN/ATM/BRCA2/CDK1/MSH6/ERCC1
## GO:0002376 MAPK9/PECAM1/XIAP/PARP1/IGFBP2/RBM15/ATM/TSC1/GAPDH/MSH6/ERCC1/TFRC
## GO:0008152 EIF4EBP1/MAPK9/EGFR/ACVRL1/PECAM1/EEF2K/RAD50/TYMS/XIAP/PARP1/ANXA7/ASNS/RBM15/PTEN/ATM/BRCA2/TSC1/TTF1/CDK1/IRS1/GAPDH/MSH6/PDK1/ERCC1/TFRC
## GO:0009987 EIF4EBP1/NRAS/MAPK9/EGFR/ACVRL1/PECAM1/RAB11A/EEF2K/RAD50/TYMS/XIAP/PARP1/ANXA7/IGFBP2/ASNS/RBM15/PTEN/ATM/BRCA2/TSC1/TTF1/CDK1/IRS1/GAPDH/MSH6/PDK1/ERCC1/TFRC
## GO:0016032 EGFR/CDK1/TFRC
## GO:0022414 EGFR/RAD50/PARP1/IGFBP2/PTEN/ATM/BRCA2/CDK1/MSH6/ERCC1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 17 17/28
## GO:0044423 GO:0044423 virion component 0 0/28
## GO:0110165 GO:0110165 cellular anatomical entity 28 28/28
## geneID
## GO:0032991 EGFR/ACVRL1/PECAM1/RAB11A/RAD50/PARP1/RBM15/ATM/BRCA2/TSC1/CDK1/IRS1/GAPDH/MSH6/PDK1/ERCC1/TFRC
## GO:0044423
## GO:0110165 EIF4EBP1/NRAS/MAPK9/EGFR/ACVRL1/PECAM1/RAB11A/EEF2K/RAD50/TYMS/XIAP/PARP1/ANXA7/IGFBP2/ASNS/RBM15/PTEN/ATM/BRCA2/TSC1/TTF1/CDK1/IRS1/GAPDH/MSH6/PDK1/ERCC1/TFRC
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/34
## GO:0003824 GO:0003824 catalytic activity 16 16/34
## GO:0005198 GO:0005198 structural molecule activity 1 1/34
## GO:0005215 GO:0005215 transporter activity 0 0/34
## GO:0005488 GO:0005488 binding 34 34/34
## GO:0009055 GO:0009055 electron transfer activity 0 0/34
## geneID
## GO:0003774 MYH11
## GO:0003824 SRC/MAPK1/GSK3A/RAB11B/XRCC1/PDK1/MAP2K1/ERCC1/G6PD/ASNS/PTEN/ATM/EGFR/VHL/GAPDH/MSH6
## GO:0005198 MYH11
## GO:0005215
## GO:0005488 AKT1S1/SRC/MAPK1/VASP/ITGA2/YWHAE/TSC1/ANLN/PDCD4/GSK3A/RAB11B/KEAP1/XRCC1/PDK1/MAP2K1/FOXM1/ERCC1/G6PD/ASNS/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/IRS1/VHL/XBP1/GAPDH/MSH6/MYH11/NF2/TFRC/PREX1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 9 9/34
## GO:0002376 GO:0002376 immune system process 16 16/34
## GO:0008152 GO:0008152 metabolic process 30 30/34
## GO:0009987 GO:0009987 cellular process 34 34/34
## GO:0016032 GO:0016032 viral process 4 4/34
## GO:0022414 GO:0022414 reproductive process 9 9/34
## geneID
## GO:0000003 SRC/ITGA2/GSK3A/ERCC1/PTEN/GATA3/ATM/EGFR/MSH6
## GO:0002376 SRC/MAPK1/ITGA2/YWHAE/TSC1/MAP2K1/ERCC1/G6PD/RBM15/GATA3/ATM/XBP1/GAPDH/MSH6/TFRC/PREX1
## GO:0008152 AKT1S1/SRC/MAPK1/ITGA2/YWHAE/TSC1/PDCD4/GSK3A/RAB11B/KEAP1/XRCC1/PDK1/MAP2K1/FOXM1/ERCC1/G6PD/ASNS/RBM15/PTEN/GATA3/ATM/EGFR/IRS1/VHL/XBP1/GAPDH/MSH6/NF2/TFRC/PREX1
## GO:0009987 AKT1S1/SRC/MAPK1/VASP/ITGA2/YWHAE/TSC1/ANLN/PDCD4/GSK3A/RAB11B/KEAP1/XRCC1/PDK1/MAP2K1/FOXM1/ERCC1/G6PD/ASNS/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/IRS1/VHL/XBP1/GAPDH/MSH6/MYH11/NF2/TFRC/PREX1
## GO:0016032 ITGA2/GSK3A/EGFR/TFRC
## GO:0022414 SRC/ITGA2/GSK3A/ERCC1/PTEN/GATA3/ATM/EGFR/MSH6
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 20 20/34
## GO:0044423 GO:0044423 virion component 0 0/34
## GO:0110165 GO:0110165 cellular anatomical entity 34 34/34
## geneID
## GO:0032991 AKT1S1/ITGA2/TSC1/GSK3A/KEAP1/XRCC1/PDK1/FOXM1/ERCC1/RBM15/GATA3/PEA15/ATM/EGFR/IRS1/XBP1/GAPDH/MSH6/MYH11/TFRC
## GO:0044423
## GO:0110165 AKT1S1/SRC/MAPK1/VASP/ITGA2/YWHAE/TSC1/ANLN/PDCD4/GSK3A/RAB11B/KEAP1/XRCC1/PDK1/MAP2K1/FOXM1/ERCC1/G6PD/ASNS/RBM15/PTEN/GATA3/PEA15/ATM/EGFR/IRS1/VHL/XBP1/GAPDH/MSH6/MYH11/NF2/TFRC/PREX1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 0 0/34
## GO:0003824 GO:0003824 catalytic activity 16 16/34
## GO:0005198 GO:0005198 structural molecule activity 1 1/34
## GO:0005215 GO:0005215 transporter activity 0 0/34
## GO:0005488 GO:0005488 binding 34 34/34
## GO:0009055 GO:0009055 electron transfer activity 0 0/34
## geneID
## GO:0003774
## GO:0003824 MAPK14/AKT3/RAD51/BIRC2/ADAR/BRCA2/PCNA/ACACB/CDK1/XRCC1/TYMS/TUBA1B/EZH2/PARP1/INPP4B/ACVRL1
## GO:0005198 TUBA1B
## GO:0005215
## GO:0005488 MAPK14/ERBB3/AKT3/CDH2/RAD51/BECN1/BIRC2/ITGA2/ADAR/BRCA2/PCNA/CTNNB1/ANLN/SHC1/STMN1/ACACB/CDK1/E2F1/XRCC1/TYMS/CCNB1/TUBA1B/NOTCH3/FOXM1/EZH2/CCNE2/ERRFI1/PARP1/RPTOR/CDKN2A/PEA15/INPP4B/ACVRL1/NF2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 9 9/34
## GO:0002376 GO:0002376 immune system process 9 9/34
## GO:0008152 GO:0008152 metabolic process 29 29/34
## GO:0009987 GO:0009987 cellular process 34 34/34
## GO:0016032 GO:0016032 viral process 4 4/34
## GO:0022414 GO:0022414 reproductive process 9 9/34
## geneID
## GO:0000003 RAD51/ITGA2/BRCA2/PCNA/CTNNB1/CDK1/CCNE2/ERRFI1/PARP1
## GO:0002376 MAPK14/BECN1/BIRC2/ITGA2/ADAR/CTNNB1/EZH2/PARP1/RPTOR
## GO:0008152 MAPK14/ERBB3/AKT3/RAD51/BECN1/BIRC2/ITGA2/ADAR/BRCA2/PCNA/CTNNB1/SHC1/ACACB/CDK1/E2F1/XRCC1/TYMS/CCNB1/NOTCH3/FOXM1/EZH2/CCNE2/ERRFI1/PARP1/RPTOR/CDKN2A/INPP4B/ACVRL1/NF2
## GO:0009987 MAPK14/ERBB3/AKT3/CDH2/RAD51/BECN1/BIRC2/ITGA2/ADAR/BRCA2/PCNA/CTNNB1/ANLN/SHC1/STMN1/ACACB/CDK1/E2F1/XRCC1/TYMS/CCNB1/TUBA1B/NOTCH3/FOXM1/EZH2/CCNE2/ERRFI1/PARP1/RPTOR/CDKN2A/PEA15/INPP4B/ACVRL1/NF2
## GO:0016032 BECN1/ITGA2/ADAR/CDK1
## GO:0022414 RAD51/ITGA2/BRCA2/PCNA/CTNNB1/CDK1/CCNE2/ERRFI1/PARP1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 25 25/34
## GO:0044423 GO:0044423 virion component 0 0/34
## GO:0110165 GO:0110165 cellular anatomical entity 34 34/34
## geneID
## GO:0032991 ERBB3/CDH2/RAD51/BECN1/BIRC2/ITGA2/ADAR/BRCA2/PCNA/CTNNB1/SHC1/ACACB/CDK1/E2F1/XRCC1/CCNB1/NOTCH3/FOXM1/EZH2/CCNE2/PARP1/RPTOR/CDKN2A/PEA15/ACVRL1
## GO:0044423
## GO:0110165 MAPK14/ERBB3/AKT3/CDH2/RAD51/BECN1/BIRC2/ITGA2/ADAR/BRCA2/PCNA/CTNNB1/ANLN/SHC1/STMN1/ACACB/CDK1/E2F1/XRCC1/TYMS/CCNB1/TUBA1B/NOTCH3/FOXM1/EZH2/CCNE2/ERRFI1/PARP1/RPTOR/CDKN2A/PEA15/INPP4B/ACVRL1/NF2
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/36
## GO:0003824 GO:0003824 catalytic activity 12 12/36
## GO:0005198 GO:0005198 structural molecule activity 3 3/36
## GO:0005215 GO:0005215 transporter activity 1 1/36
## GO:0005488 GO:0005488 binding 34 34/36
## GO:0009055 GO:0009055 electron transfer activity 0 0/36
## geneID
## GO:0003774 MYH9
## GO:0003824 AKT2/AXL/MAPK1/BIRC2/XRCC5/PTK2/LCK/RAB25/PARP1/CASP9/NAPSA/SYK
## GO:0005198 CLDN7/CTNNA1/KRT5
## GO:0005215 KCNJ13
## GO:0005488 ERBB3/EIF4EBP1/AKT2/CLDN7/ESR1/GATA3/EIF4G1/AXL/MAPK1/BIRC2/XRCC5/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/CTNNA1/TP63/NRG1/KRT5/MYH9/YWHAB/RAB25/BID/TFRC/ERRFI1/PARP1/CASP9/NAPSA/SYK/TFF1/MACC1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 8 8/36
## GO:0002376 GO:0002376 immune system process 16 16/36
## GO:0008152 GO:0008152 metabolic process 28 28/36
## GO:0009987 GO:0009987 cellular process 35 35/36
## GO:0016032 GO:0016032 viral process 2 2/36
## GO:0022414 GO:0022414 reproductive process 8 8/36
## geneID
## GO:0000003 ESR1/GATA3/AXL/CTNNA1/TP63/MYH9/ERRFI1/PARP1
## GO:0002376 ESR1/GATA3/AXL/MAPK1/BIRC2/XRCC5/LCN2/PTK2/MS4A1/LCK/MYH9/BID/TFRC/PARP1/SYK/CHGA
## GO:0008152 ERBB3/EIF4EBP1/AKT2/ESR1/GATA3/EIF4G1/AXL/MAPK1/BIRC2/XRCC5/LCN2/CDH3/PDCD4/PTK2/LCK/TP63/NRG1/MYH9/YWHAB/BID/TFRC/ERRFI1/PARP1/CASP9/NAPSA/SYK/TFF1/MACC1
## GO:0009987 ERBB3/EIF4EBP1/AKT2/CLDN7/ESR1/GATA3/EIF4G1/AXL/MAPK1/BIRC2/XRCC5/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/CTNNA1/TP63/NRG1/KRT5/MYH9/YWHAB/RAB25/BID/TFRC/ERRFI1/PARP1/CASP9/SYK/TFF1/MACC1/CHGA/KCNJ13
## GO:0016032 AXL/TFRC
## GO:0022414 ESR1/GATA3/AXL/CTNNA1/TP63/MYH9/ERRFI1/PARP1
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 16 16/36
## GO:0044423 GO:0044423 virion component 0 0/36
## GO:0110165 GO:0110165 cellular anatomical entity 36 36/36
## geneID
## GO:0032991 ERBB3/ESR1/GATA3/EIF4G1/AXL/BIRC2/XRCC5/CDH3/CTNNA1/TP63/MYH9/TFRC/PARP1/CASP9/SYK/KCNJ13
## GO:0044423
## GO:0110165 ERBB3/EIF4EBP1/AKT2/CLDN7/ESR1/GATA3/EIF4G1/AXL/MAPK1/BIRC2/XRCC5/LCN2/CDH3/PDCD4/PTK2/PRRT2/MS4A1/LCK/CTNNA1/TP63/NRG1/KRT5/MYH9/YWHAB/RAB25/BID/TFRC/ERRFI1/PARP1/CASP9/NAPSA/SYK/TFF1/MACC1/CHGA/KCNJ13
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/44
## GO:0003824 GO:0003824 catalytic activity 19 19/44
## GO:0005198 GO:0005198 structural molecule activity 2 2/44
## GO:0005215 GO:0005215 transporter activity 1 1/44
## GO:0005488 GO:0005488 binding 44 44/44
## GO:0009055 GO:0009055 electron transfer activity 0 0/44
## geneID
## GO:0003774 MYH9
## GO:0003824 CASP3/ATM/XIAP/MAPK8/TUBA1B/INPP4B/MAPK1/FASN/CDKN1A/NRAS/ADAR/CCND1/PARP1/EEF2/MTOR/GSK3B/IGF1R/PRDX1/PRKAA1
## GO:0005198 TUBA1B/CTNNA1
## GO:0005215 IGF1R
## GO:0005488 CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/YWHAZ/EIF4G1/YWHAE/ARID1A/NDRG1/INPP4B/TP53/AR/MAPK1/FASN/CDKN1A/STAT5A/NF2/NRAS/ADAR/PREX1/MYH9/CCND1/CDKN1B/BCL2L11/PARP1/ANXA7/CTNNA1/EEF2/MTOR/GSK3B/IGF1R/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/SYP/TFRC/WWTR1/YWHAB/MACC1
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 11 11/44
## GO:0002376 GO:0002376 immune system process 21 21/44
## GO:0008152 GO:0008152 metabolic process 37 37/44
## GO:0009987 GO:0009987 cellular process 44 44/44
## GO:0016032 GO:0016032 viral process 4 4/44
## GO:0022414 GO:0022414 reproductive process 11 11/44
## geneID
## GO:0000003 CASP3/ATM/SMAD4/AR/MYH9/CDKN1B/BCL2L11/PARP1/CTNNA1/MTOR/IGF1R
## GO:0002376 CASP3/ATM/XIAP/MAPK8/YWHAZ/YWHAE/ARID1A/NDRG1/TP53/MAPK1/CDKN1A/ADAR/PREX1/MYH9/BCL2L11/PARP1/MTOR/IGF1R/PRDX1/SERPINE1/TFRC
## GO:0008152 CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/YWHAZ/EIF4G1/YWHAE/ARID1A/INPP4B/TP53/AR/MAPK1/FASN/CDKN1A/STAT5A/NF2/ADAR/PREX1/MYH9/CCND1/CDKN1B/PARP1/ANXA7/EEF2/MTOR/GSK3B/IGF1R/PRDX1/SERPINE1/PRKAA1/SRSF1/TFRC/WWTR1/YWHAB/MACC1
## GO:0009987 CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/YWHAZ/EIF4G1/YWHAE/ARID1A/NDRG1/INPP4B/TP53/AR/MAPK1/FASN/CDKN1A/STAT5A/NF2/NRAS/ADAR/PREX1/MYH9/CCND1/CDKN1B/BCL2L11/PARP1/ANXA7/CTNNA1/EEF2/MTOR/GSK3B/IGF1R/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/SYP/TFRC/WWTR1/YWHAB/MACC1
## GO:0016032 TP53/ADAR/GSK3B/TFRC
## GO:0022414 CASP3/ATM/SMAD4/AR/MYH9/CDKN1B/BCL2L11/PARP1/CTNNA1/MTOR/IGF1R
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 27 27/44
## GO:0044423 GO:0044423 virion component 0 0/44
## GO:0110165 GO:0110165 cellular anatomical entity 44 44/44
## geneID
## GO:0032991 CASP3/CDH1/ATM/SMAD4/EIF4G1/ARID1A/TP53/AR/CDKN1A/STAT5A/ADAR/MYH9/CCND1/CDKN1B/BCL2L11/PARP1/CTNNA1/EEF2/MTOR/GSK3B/IGF1R/SERPINE1/PRKAA1/PXN/SRSF1/TFRC/WWTR1
## GO:0044423
## GO:0110165 CASP3/CDH1/ATM/XIAP/SMAD4/MAPK8/TUBA1B/YWHAZ/EIF4G1/YWHAE/ARID1A/NDRG1/INPP4B/TP53/AR/MAPK1/FASN/CDKN1A/STAT5A/NF2/NRAS/ADAR/PREX1/MYH9/CCND1/CDKN1B/BCL2L11/PARP1/ANXA7/CTNNA1/EEF2/MTOR/GSK3B/IGF1R/PRDX1/SERPINE1/PRKAA1/PXN/SRSF1/SYP/TFRC/WWTR1/YWHAB/MACC1
## ID Description Count GeneRatio
## GO:0003774 GO:0003774 cytoskeletal motor activity 1 1/72
## GO:0003824 GO:0003824 catalytic activity 39 39/72
## GO:0005198 GO:0005198 structural molecule activity 2 2/72
## GO:0005215 GO:0005215 transporter activity 1 1/72
## GO:0005488 GO:0005488 binding 71 71/72
## GO:0009055 GO:0009055 electron transfer activity 0 0/72
## geneID
## GO:0003774 MYH9
## GO:0003824 CCNE1/PTEN/PIK3R1/CDK1/IDH3A/RAD51/RPS6KB1/TUBA1B/MAPK14/NRAS/ADAR/CCND1/CDKN1A/EGFR/ARAF/MSH2/EZH2/MAPK9/BRCA2/PTGS2/TYMS/AKT2/MAP2K1/AKT3/BIRC2/EEF2/GSK3B/IGF1R/PCNA/PRKAA1/PRKCA/MAPK3/MAPK8/TGM2/RAB11A/INPP4B/FASN/RAB11B/BRAF
## GO:0005198 TUBA1B/CTNNA1
## GO:0005215 IGF1R
## GO:0005488 CCNE1/PTEN/CAV1/PIK3R1/CDK1/IDH3A/ITGA2/RAD51/RPS6KB1/SRSF1/PEA15/TUBA1B/MAPK14/E2F1/NRAS/ADAR/MYH9/CCND1/CDKN1A/IRS1/MYC/EGFR/TP63/ARAF/JUN/MSH2/EZH2/MAPK9/PIK3R2/BRCA2/PTGS2/TYMS/TP53/AKT2/MAP2K1/NFKB1/ERRFI1/AKT3/BIRC2/CCNB1/CTNNA1/CTNNB1/EEF2/EIF4G1/FOXM1/GSK3B/IGF1R/IGFBP2/SMAD4/SERPINE1/PCNA/PRKAA1/PRKCA/MAPK3/MAPK8/PXN/TFRC/TGM2/ARID1A/BECN1/RAB11A/SQSTM1/ANLN/INPP4B/YWHAB/FASN/RAB11B/BRAF/PRRT2/MACC1/NF2
## GO:0009055
## ID Description Count GeneRatio
## GO:0000003 GO:0000003 reproduction 19 19/72
## GO:0002376 GO:0002376 immune system process 30 30/72
## GO:0008152 GO:0008152 metabolic process 62 62/72
## GO:0009987 GO:0009987 cellular process 72 72/72
## GO:0016032 GO:0016032 viral process 10 10/72
## GO:0022414 GO:0022414 reproductive process 19 19/72
## geneID
## GO:0000003 CCNE1/PTEN/CDK1/ITGA2/RAD51/RPS6KB1/MYH9/EGFR/TP63/MSH2/BRCA2/PTGS2/ERRFI1/CTNNA1/CTNNB1/IGF1R/IGFBP2/SMAD4/PCNA
## GO:0002376 CAV1/PIK3R1/ITGA2/RPS6KB1/CHGA/MAPK14/ADAR/MYH9/CDKN1A/MYC/MSH2/EZH2/MAPK9/PIK3R2/TP53/MAP2K1/NFKB1/BIRC2/CTNNB1/IGF1R/IGFBP2/SERPINE1/PRKCA/MAPK3/MAPK8/TFRC/ARID1A/BECN1/SQSTM1/BRAF
## GO:0008152 CCNE1/PTEN/CAV1/PIK3R1/CDK1/IDH3A/ITGA2/RAD51/RPS6KB1/SRSF1/MAPK14/E2F1/ADAR/MYH9/CCND1/CDKN1A/IRS1/MYC/EGFR/TP63/ARAF/JUN/MSH2/EZH2/MAPK9/PIK3R2/BRCA2/PTGS2/TYMS/TP53/AKT2/MAP2K1/NFKB1/ERRFI1/AKT3/BIRC2/CCNB1/CTNNB1/EEF2/EIF4G1/FOXM1/GSK3B/IGF1R/SMAD4/SERPINE1/PCNA/PRKAA1/PRKCA/MAPK3/MAPK8/TFRC/TGM2/ARID1A/BECN1/SQSTM1/INPP4B/YWHAB/FASN/RAB11B/BRAF/MACC1/NF2
## GO:0009987 CCNE1/PTEN/CAV1/PIK3R1/CDK1/IDH3A/ITGA2/RAD51/RPS6KB1/SRSF1/PEA15/TUBA1B/CHGA/MAPK14/E2F1/NRAS/ADAR/MYH9/CCND1/CDKN1A/IRS1/MYC/EGFR/TP63/ARAF/JUN/MSH2/EZH2/MAPK9/PIK3R2/BRCA2/PTGS2/TYMS/TP53/AKT2/MAP2K1/NFKB1/ERRFI1/AKT3/BIRC2/CCNB1/CTNNA1/CTNNB1/EEF2/EIF4G1/FOXM1/GSK3B/IGF1R/IGFBP2/SMAD4/SERPINE1/PCNA/PRKAA1/PRKCA/MAPK3/MAPK8/PXN/TFRC/TGM2/ARID1A/BECN1/RAB11A/SQSTM1/ANLN/INPP4B/YWHAB/FASN/RAB11B/BRAF/PRRT2/MACC1/NF2
## GO:0016032 CAV1/CDK1/ITGA2/ADAR/EGFR/JUN/TP53/GSK3B/TFRC/BECN1
## GO:0022414 CCNE1/PTEN/CDK1/ITGA2/RAD51/RPS6KB1/MYH9/EGFR/TP63/MSH2/BRCA2/PTGS2/ERRFI1/CTNNA1/CTNNB1/IGF1R/IGFBP2/SMAD4/PCNA
## ID Description Count GeneRatio
## GO:0032991 GO:0032991 protein-containing complex 46 46/72
## GO:0044423 GO:0044423 virion component 0 0/72
## GO:0110165 GO:0110165 cellular anatomical entity 72 72/72
## geneID
## GO:0032991 CCNE1/CAV1/PIK3R1/CDK1/IDH3A/ITGA2/RAD51/SRSF1/PEA15/E2F1/ADAR/MYH9/CCND1/CDKN1A/IRS1/MYC/EGFR/TP63/JUN/MSH2/EZH2/PIK3R2/BRCA2/PTGS2/TP53/NFKB1/BIRC2/CCNB1/CTNNA1/CTNNB1/EEF2/EIF4G1/FOXM1/GSK3B/IGF1R/SMAD4/SERPINE1/PCNA/PRKAA1/PRKCA/PXN/TFRC/TGM2/ARID1A/BECN1/RAB11A
## GO:0044423
## GO:0110165 CCNE1/PTEN/CAV1/PIK3R1/CDK1/IDH3A/ITGA2/RAD51/RPS6KB1/SRSF1/PEA15/TUBA1B/CHGA/MAPK14/E2F1/NRAS/ADAR/MYH9/CCND1/CDKN1A/IRS1/MYC/EGFR/TP63/ARAF/JUN/MSH2/EZH2/MAPK9/PIK3R2/BRCA2/PTGS2/TYMS/TP53/AKT2/MAP2K1/NFKB1/ERRFI1/AKT3/BIRC2/CCNB1/CTNNA1/CTNNB1/EEF2/EIF4G1/FOXM1/GSK3B/IGF1R/IGFBP2/SMAD4/SERPINE1/PCNA/PRKAA1/PRKCA/MAPK3/MAPK8/PXN/TFRC/TGM2/ARID1A/BECN1/RAB11A/SQSTM1/ANLN/INPP4B/YWHAB/FASN/RAB11B/BRAF/PRRT2/MACC1/NF2barplot(ggo_MF[[1]], title = "groupGO, Molecular Function, Factor 1 of 1")
barplot(ggo_MF[[2]], title = "groupGO, Molecular Function, Factor 1 of 2")
barplot(ggo_MF[[3]], title = "groupGO, Molecular Function, Factor 2 of 2")
barplot(ggo_MF[[4]], title = "groupGO, Molecular Function, Factor 1 of 3")
barplot(ggo_MF[[5]], title = "groupGO, Molecular Function, Factor 2 of 3")
barplot(ggo_MF[[6]], title = "groupGO, Molecular Function, Factor 3 of 3")
barplot(ggo_MF[[7]], title = "groupGO, Molecular Function, Factor 1 of 5")
barplot(ggo_MF[[8]], title = "groupGO, Molecular Function, Factor 2 of 5")
barplot(ggo_MF[[9]], title = "groupGO, Molecular Function, Factor 3 of 5")
barplot(ggo_MF[[10]], title = "groupGO, Molecular Function, Factor 4 of 5")
barplot(ggo_MF[[11]], title = "groupGO, Molecular Function, Factor 5 of 5")
barplot(ggo_MF[[12]], title = "groupGO, Molecular Function, Factor 1 of 10")
barplot(ggo_MF[[13]], title = "groupGO, Molecular Function, Factor 2 of 10")
barplot(ggo_MF[[14]], title = "groupGO, Molecular Function, Factor 3 of 10")
barplot(ggo_MF[[15]], title = "groupGO, Molecular Function, Factor 4 of 10")
barplot(ggo_MF[[16]], title = "groupGO, Molecular Function, Factor 5 of 10")
barplot(ggo_MF[[17]], title = "groupGO, Molecular Function, Factor 6 of 10")
barplot(ggo_MF[[18]], title = "groupGO, Molecular Function, Factor 7 of 10")
barplot(ggo_MF[[19]], title = "groupGO, Molecular Function, Factor 8 of 10")
barplot(ggo_MF[[20]], title = "groupGO, Molecular Function, Factor 9 of 10")
barplot(ggo_MF[[21]], title = "groupGO, Molecular Function, Factor 10 of 10")
barplot(ggo_BP[[1]], title = "groupGO, Biological Process, Factor 1 of 1")
barplot(ggo_BP[[2]], title = "groupGO, Biological Process, Factor 1 of 2")
barplot(ggo_BP[[3]], title = "groupGO, Biological Process, Factor 2 of 2")
barplot(ggo_BP[[4]], title = "groupGO, Biological Process, Factor 1 of 3")
barplot(ggo_BP[[5]], title = "groupGO, Biological Process, Factor 2 of 3")
barplot(ggo_BP[[6]], title = "groupGO, Biological Process, Factor 3 of 3")
barplot(ggo_BP[[7]], title = "groupGO, Biological Process, Factor 1 of 5")
barplot(ggo_BP[[8]], title = "groupGO, Biological Process, Factor 2 of 5")
barplot(ggo_BP[[9]], title = "groupGO, Biological Process, Factor 3 of 5")
barplot(ggo_BP[[10]], title = "groupGO, Biological Process, Factor 4 of 5")
barplot(ggo_BP[[11]], title = "groupGO, Biological Process, Factor 5 of 5")
barplot(ggo_BP[[12]], title = "groupGO, Biological Process, Factor 1 of 10")
barplot(ggo_BP[[13]], title = "groupGO, Biological Process, Factor 2 of 10")
barplot(ggo_BP[[14]], title = "groupGO, Biological Process, Factor 3 of 10")
barplot(ggo_BP[[15]], title = "groupGO, Biological Process, Factor 4 of 10")
barplot(ggo_BP[[16]], title = "groupGO, Biological Process, Factor 5 of 10")
barplot(ggo_BP[[17]], title = "groupGO, Biological Process, Factor 6 of 10")
barplot(ggo_BP[[18]], title = "groupGO, Biological Process, Factor 7 of 10")
barplot(ggo_BP[[19]], title = "groupGO, Biological Process, Factor 8 of 10")
barplot(ggo_BP[[20]], title = "groupGO, Biological Process, Factor 9 of 10")
barplot(ggo_BP[[21]], title = "groupGO, Biological Process, Factor 10 of 10")
barplot(ggo_CC[[1]], title = "groupGO, Cellular Component, Factor 1 of 1")
barplot(ggo_CC[[2]], title = "groupGO, Cellular Component, Factor 1 of 2")
barplot(ggo_CC[[3]], title = "groupGO, Cellular Component, Factor 2 of 2")
barplot(ggo_CC[[4]], title = "groupGO, Cellular Component, Factor 1 of 3")
barplot(ggo_CC[[5]], title = "groupGO, Cellular Component, Factor 2 of 3")
barplot(ggo_CC[[6]], title = "groupGO, Cellular Component, Factor 3 of 3")
barplot(ggo_CC[[7]], title = "groupGO, Cellular Component, Factor 1 of 5")
barplot(ggo_CC[[8]], title = "groupGO, Cellular Component, Factor 2 of 5")
barplot(ggo_CC[[9]], title = "groupGO, Cellular Component, Factor 3 of 5")
barplot(ggo_CC[[10]], title = "groupGO, Cellular Component, Factor 4 of 5")
barplot(ggo_CC[[11]], title = "groupGO, Cellular Component, Factor 5 of 5")
barplot(ggo_CC[[12]], title = "groupGO, Cellular Component, Factor 1 of 10")
barplot(ggo_CC[[13]], title = "groupGO, Cellular Component, Factor 2 of 10")
barplot(ggo_CC[[14]], title = "groupGO, Cellular Component, Factor 3 of 10")
barplot(ggo_CC[[15]], title = "groupGO, Cellular Component, Factor 4 of 10")
barplot(ggo_CC[[16]], title = "groupGO, Cellular Component, Factor 5 of 10")
barplot(ggo_CC[[17]], title = "groupGO, Cellular Component, Factor 6 of 10")
barplot(ggo_CC[[18]], title = "groupGO, Cellular Component, Factor 7 of 10")
barplot(ggo_CC[[19]], title = "groupGO, Cellular Component, Factor 8 of 10")
barplot(ggo_CC[[20]], title = "groupGO, Cellular Component, Factor 9 of 10")
barplot(ggo_CC[[21]], title = "groupGO, Cellular Component, Factor 10 of 10")
B. GO Over-Representation
ego_MF <- list()#GO enrichment of a geneset for Molecular Function
ego_BP <- list()#GO enrichment of a geneset for Biological Process
ego_CC <- list()#GO enrichment of a geneset for Cellular Component
for(z in 1:length(geneNames)){
print(z)
input <- geneNames[[z]]
ego_MF[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "MF",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_BP[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "BP",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
ego_CC[[z]] <- enrichGO(
gene = input,
OrgDb = org.Hs.eg.db,
ont = "CC",
pAdjustMethod = "BH",
keyType="SYMBOL",
pvalueCutoff = 0.05,
qvalueCutoff = 0.05,
minGSSize = 2,
readable = TRUE)
}## [1] 1
## [1] 2
## [1] 3
## [1] 4
## [1] 5
## [1] 6
## [1] 7
## [1] 8
## [1] 9
## [1] 10
## [1] 11
## [1] 12
## [1] 13
## [1] 14
## [1] 15
## [1] 16
## [1] 17
## [1] 18
## [1] 19
## [1] 20
## [1] 21for(z in 1:length(geneNames)){
print(head(ego_MF[[z]]))
print(head(ego_BP[[z]]))
print(head(ego_CC[[z]]))
}## ID Description GeneRatio
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 2/23
## GO:0106310 GO:0106310 protein serine kinase activity 5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 5/23
## GO:0004707 GO:0004707 MAP kinase activity 2/23
## GO:0070064 GO:0070064 proline-rich region binding 2/23
## GO:0042826 GO:0042826 histone deacetylase binding 3/23
## BgRatio pvalue p.adjust qvalue
## GO:0120283 7/18522 3.085855e-05 0.005523681 0.002273788
## GO:0106310 363/18522 7.075911e-05 0.006332941 0.002606915
## GO:0004674 427/18522 1.518718e-04 0.007100610 0.002922921
## GO:0004707 16/18522 1.751391e-04 0.007100610 0.002922921
## GO:0070064 17/18522 1.983411e-04 0.007100610 0.002922921
## GO:0042826 128/18522 5.160029e-04 0.015394085 0.006336877
## geneID Count
## GO:0120283 MAPK8/XIAP 2
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004707 MAPK8/MAPK1 2
## GO:0070064 CCND1/YAP1 2
## GO:0042826 HSPA1A/MAPK8/CCND1 3
## ID Description GeneRatio
## GO:0010631 GO:0010631 epithelial cell migration 9/23
## GO:0090132 GO:0090132 epithelium migration 9/23
## GO:0090130 GO:0090130 tissue migration 9/23
## GO:0001667 GO:0001667 ameboidal-type cell migration 9/23
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus 8/23
## BgRatio pvalue p.adjust qvalue
## GO:0010631 375/18888 2.784961e-10 2.143530e-07 8.314100e-08
## GO:0090132 378/18888 2.988249e-10 2.143530e-07 8.314100e-08
## GO:0090130 383/18888 3.356258e-10 2.143530e-07 8.314100e-08
## GO:0001667 498/18888 3.370825e-09 1.092718e-06 4.238319e-07
## GO:0071214 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## GO:0104004 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 6/23 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 6/23 431/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/23 4/19894
## GO:0070938 GO:0070938 contractile ring 2/23 10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 4/23 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 4/23 248/19894
## pvalue p.adjust qvalue
## GO:0005925 6.447048e-06 0.0003166418 0.0001720295
## GO:0030055 7.373490e-06 0.0003166418 0.0001720295
## GO:0005826 7.660689e-06 0.0003166418 0.0001720295
## GO:0070938 5.721303e-05 0.0017736039 0.0009635879
## GO:0005741 1.073470e-04 0.0026622052 0.0014463593
## GO:0031968 1.732117e-04 0.0031642699 0.0017191279
## geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1 6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1 6
## GO:0005826 MYH9/ANLN 2
## GO:0070938 MYH9/ANLN 2
## GO:0005741 MTOR/FOXO3/CASP8/KRAS 4
## GO:0031968 MTOR/FOXO3/CASP8/KRAS 4
## ID Description GeneRatio
## GO:0032143 GO:0032143 single thymine insertion binding 2/27
## GO:0032137 GO:0032137 guanine/thymine mispair binding 2/27
## GO:0032142 GO:0032142 single guanine insertion binding 2/27
## GO:0032138 GO:0032138 single base insertion or deletion binding 2/27
## GO:0097718 GO:0097718 disordered domain specific binding 3/27
## GO:0032135 GO:0032135 DNA insertion or deletion binding 2/27
## BgRatio pvalue p.adjust qvalue geneID
## GO:0032143 2/18522 2.046373e-06 0.0003864164 0.0001743232 MSH6/MSH2
## GO:0032137 3/18522 6.133594e-06 0.0003864164 0.0001743232 MSH6/MSH2
## GO:0032142 3/18522 6.133594e-06 0.0003864164 0.0001743232 MSH6/MSH2
## GO:0032138 4/18522 1.225615e-05 0.0005035163 0.0002271502 MSH6/MSH2
## GO:0097718 32/18522 1.332054e-05 0.0005035163 0.0002271502 RB1/NCOA3/GAPDH
## GO:0032135 6/18522 3.058526e-05 0.0008258020 0.0003725423 MSH6/MSH2
## Count
## GO:0032143 2
## GO:0032137 2
## GO:0032142 2
## GO:0032138 2
## GO:0097718 3
## GO:0032135 2
## ID
## GO:0051402 GO:0051402
## GO:0045785 GO:0045785
## GO:0008630 GO:0008630
## GO:0043254 GO:0043254
## GO:0030099 GO:0030099
## GO:0002562 GO:0002562
## Description
## GO:0051402 neuron apoptotic process
## GO:0045785 positive regulation of cell adhesion
## GO:0008630 intrinsic apoptotic signaling pathway in response to DNA damage
## GO:0043254 regulation of protein-containing complex assembly
## GO:0030099 myeloid cell differentiation
## GO:0002562 somatic diversification of immune receptors via germline recombination within a single locus
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051402 7/27 292/18888 1.338203e-07 0.0001484232 8.674955e-05
## GO:0045785 8/27 485/18888 2.577809e-07 0.0001484232 8.674955e-05
## GO:0008630 5/27 102/18888 3.056072e-07 0.0001484232 8.674955e-05
## GO:0043254 7/27 418/18888 1.497283e-06 0.0005244227 3.065115e-04
## GO:0030099 7/27 439/18888 2.073983e-06 0.0005244227 3.065115e-04
## GO:0002562 4/27 70/18888 2.846143e-06 0.0005244227 3.065115e-04
## geneID Count
## GO:0051402 RB1/XIAP/BID/G6PD/ATM/GAPDH/MSH2 7
## GO:0045785 ETS1/ARID1A/IGFBP2/ATM/TSC1/XBP1/TFRC/PREX1 8
## GO:0008630 BID/ATM/BRCA2/MSH6/MSH2 5
## GO:0043254 RB1/MAPK8/BID/STMN1/ATM/TFRC/PREX1 7
## GO:0030099 RB1/ETS1/GAB2/G6PD/RBM15/FASN/TFRC 7
## GO:0002562 ATM/MSH6/TFRC/MSH2 4
## ID Description GeneRatio BgRatio pvalue
## GO:0032301 GO:0032301 MutSalpha complex 2/27 2/19894 1.773841e-06
## GO:0032300 GO:0032300 mismatch repair complex 2/27 11/19894 9.682824e-05
## GO:1990391 GO:1990391 DNA repair complex 2/27 22/19894 4.029496e-04
## GO:0042470 GO:0042470 melanosome 3/27 112/19894 4.604156e-04
## GO:0048770 GO:0048770 pigment granule 3/27 112/19894 4.604156e-04
## GO:0016514 GO:0016514 SWI/SNF complex 2/27 30/19894 7.537380e-04
## p.adjust qvalue geneID Count
## GO:0032301 0.000200444 0.0001456417 MSH6/MSH2 2
## GO:0032300 0.005470795 0.0039750539 MSH6/MSH2 2
## GO:1990391 0.010405392 0.0075605085 ATM/BRCA2 2
## GO:0042470 0.010405392 0.0075605085 FASN/PRDX1/TFRC 3
## GO:0048770 0.010405392 0.0075605085 FASN/PRDX1/TFRC 3
## GO:0016514 0.014195400 0.0103143099 RB1/ARID1A 2
## ID Description GeneRatio
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 2/23
## GO:0106310 GO:0106310 protein serine kinase activity 5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 5/23
## GO:0004707 GO:0004707 MAP kinase activity 2/23
## GO:0070064 GO:0070064 proline-rich region binding 2/23
## GO:0042826 GO:0042826 histone deacetylase binding 3/23
## BgRatio pvalue p.adjust qvalue
## GO:0120283 7/18522 3.085855e-05 0.005523681 0.002273788
## GO:0106310 363/18522 7.075911e-05 0.006332941 0.002606915
## GO:0004674 427/18522 1.518718e-04 0.007100610 0.002922921
## GO:0004707 16/18522 1.751391e-04 0.007100610 0.002922921
## GO:0070064 17/18522 1.983411e-04 0.007100610 0.002922921
## GO:0042826 128/18522 5.160029e-04 0.015394085 0.006336877
## geneID Count
## GO:0120283 MAPK8/XIAP 2
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004707 MAPK8/MAPK1 2
## GO:0070064 CCND1/YAP1 2
## GO:0042826 HSPA1A/MAPK8/CCND1 3
## ID Description GeneRatio
## GO:0010631 GO:0010631 epithelial cell migration 9/23
## GO:0090132 GO:0090132 epithelium migration 9/23
## GO:0090130 GO:0090130 tissue migration 9/23
## GO:0001667 GO:0001667 ameboidal-type cell migration 9/23
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus 8/23
## BgRatio pvalue p.adjust qvalue
## GO:0010631 375/18888 2.784961e-10 2.143530e-07 8.314100e-08
## GO:0090132 378/18888 2.988249e-10 2.143530e-07 8.314100e-08
## GO:0090130 383/18888 3.356258e-10 2.143530e-07 8.314100e-08
## GO:0001667 498/18888 3.370825e-09 1.092718e-06 4.238319e-07
## GO:0071214 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## GO:0104004 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 6/23 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 6/23 431/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/23 4/19894
## GO:0070938 GO:0070938 contractile ring 2/23 10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 4/23 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 4/23 248/19894
## pvalue p.adjust qvalue
## GO:0005925 6.447048e-06 0.0003166418 0.0001720295
## GO:0030055 7.373490e-06 0.0003166418 0.0001720295
## GO:0005826 7.660689e-06 0.0003166418 0.0001720295
## GO:0070938 5.721303e-05 0.0017736039 0.0009635879
## GO:0005741 1.073470e-04 0.0026622052 0.0014463593
## GO:0031968 1.732117e-04 0.0031642699 0.0017191279
## geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1 6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1 6
## GO:0005826 MYH9/ANLN 2
## GO:0070938 MYH9/ANLN 2
## GO:0005741 MTOR/FOXO3/CASP8/KRAS 4
## GO:0031968 MTOR/FOXO3/CASP8/KRAS 4
## ID Description GeneRatio
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 2/23
## GO:0106310 GO:0106310 protein serine kinase activity 5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 5/23
## GO:0004707 GO:0004707 MAP kinase activity 2/23
## GO:0070064 GO:0070064 proline-rich region binding 2/23
## GO:0042826 GO:0042826 histone deacetylase binding 3/23
## BgRatio pvalue p.adjust qvalue
## GO:0120283 7/18522 3.085855e-05 0.005523681 0.002273788
## GO:0106310 363/18522 7.075911e-05 0.006332941 0.002606915
## GO:0004674 427/18522 1.518718e-04 0.007100610 0.002922921
## GO:0004707 16/18522 1.751391e-04 0.007100610 0.002922921
## GO:0070064 17/18522 1.983411e-04 0.007100610 0.002922921
## GO:0042826 128/18522 5.160029e-04 0.015394085 0.006336877
## geneID Count
## GO:0120283 MAPK8/XIAP 2
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004707 MAPK8/MAPK1 2
## GO:0070064 CCND1/YAP1 2
## GO:0042826 HSPA1A/MAPK8/CCND1 3
## ID Description GeneRatio
## GO:0010631 GO:0010631 epithelial cell migration 9/23
## GO:0090132 GO:0090132 epithelium migration 9/23
## GO:0090130 GO:0090130 tissue migration 9/23
## GO:0001667 GO:0001667 ameboidal-type cell migration 9/23
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus 8/23
## BgRatio pvalue p.adjust qvalue
## GO:0010631 375/18888 2.784961e-10 2.143530e-07 8.314100e-08
## GO:0090132 378/18888 2.988249e-10 2.143530e-07 8.314100e-08
## GO:0090130 383/18888 3.356258e-10 2.143530e-07 8.314100e-08
## GO:0001667 498/18888 3.370825e-09 1.092718e-06 4.238319e-07
## GO:0071214 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## GO:0104004 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 6/23 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 6/23 431/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/23 4/19894
## GO:0070938 GO:0070938 contractile ring 2/23 10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 4/23 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 4/23 248/19894
## pvalue p.adjust qvalue
## GO:0005925 6.447048e-06 0.0003166418 0.0001720295
## GO:0030055 7.373490e-06 0.0003166418 0.0001720295
## GO:0005826 7.660689e-06 0.0003166418 0.0001720295
## GO:0070938 5.721303e-05 0.0017736039 0.0009635879
## GO:0005741 1.073470e-04 0.0026622052 0.0014463593
## GO:0031968 1.732117e-04 0.0031642699 0.0017191279
## geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1 6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1 6
## GO:0005826 MYH9/ANLN 2
## GO:0070938 MYH9/ANLN 2
## GO:0005741 MTOR/FOXO3/CASP8/KRAS 4
## GO:0031968 MTOR/FOXO3/CASP8/KRAS 4
## ID
## GO:0140297 GO:0140297
## GO:0120283 GO:0120283
## GO:0031625 GO:0031625
## GO:0044389 GO:0044389
## GO:0140311 GO:0140311
## GO:0061629 GO:0061629
## Description
## GO:0140297 DNA-binding transcription factor binding
## GO:0120283 protein serine/threonine kinase binding
## GO:0031625 ubiquitin protein ligase binding
## GO:0044389 ubiquitin-like protein ligase binding
## GO:0140311 protein sequestering activity
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0140297 6/20 478/18522 8.157340e-06 0.001231758 0.0005495471
## GO:0120283 2/20 7/18522 2.318693e-05 0.001750613 0.0007810334
## GO:0031625 4/20 305/18522 2.836004e-04 0.011142865 0.0049713724
## GO:0044389 4/20 324/18522 3.568288e-04 0.011142865 0.0049713724
## GO:0140311 2/20 29/18522 4.419377e-04 0.011142865 0.0049713724
## GO:0061629 4/20 343/18522 4.427629e-04 0.011142865 0.0049713724
## geneID Count
## GO:0140297 RB1/ETS1/ARID1A/YWHAZ/NCOA3/VHL 6
## GO:0120283 XIAP/MAPK8 2
## GO:0031625 RB1/BID/YWHAZ/CDKN1A 4
## GO:0044389 RB1/BID/YWHAZ/CDKN1A 4
## GO:0140311 YWHAZ/CDKN1A 2
## GO:0061629 RB1/ETS1/ARID1A/NCOA3 4
## ID
## GO:2000045 GO:2000045
## GO:1902806 GO:1902806
## GO:0000082 GO:0000082
## GO:0044843 GO:0044843
## GO:2000134 GO:2000134
## GO:1902807 GO:1902807
## Description
## GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 regulation of cell cycle G1/S phase transition
## GO:0000082 G1/S transition of mitotic cell cycle
## GO:0044843 cell cycle G1/S phase transition
## GO:2000134 negative regulation of G1/S transition of mitotic cell cycle
## GO:1902807 negative regulation of cell cycle G1/S phase transition
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:2000045 7/20 185/18888 5.372413e-10 7.220523e-07 3.472275e-07
## GO:1902806 7/20 211/18888 1.346798e-09 9.050483e-07 4.352284e-07
## GO:0000082 7/20 234/18888 2.767587e-09 1.239879e-06 5.962451e-07
## GO:0044843 7/20 262/18888 6.061003e-09 2.036497e-06 9.793305e-07
## GO:2000134 5/20 85/18888 2.408730e-08 6.474667e-06 3.113601e-06
## GO:1902807 5/20 94/18888 4.006836e-08 8.975312e-06 4.316135e-06
## geneID Count
## GO:2000045 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 7
## GO:1902806 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 7
## GO:0000082 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 7
## GO:0044843 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 7
## GO:2000134 RB1/PTEN/ATM/CCND1/CDKN1A 5
## GO:1902807 RB1/PTEN/ATM/CCND1/CDKN1A 5
## ID Description
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:1902554 GO:1902554 serine/threonine protein kinase complex
## GO:0016514 GO:0016514 SWI/SNF complex
## GO:1902911 GO:1902911 protein kinase complex
## GO:0005925 GO:0005925 focal adhesion
## GO:0030055 GO:0030055 cell-substrate junction
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0000307 3/20 56/19894 2.328041e-05 0.002165078 0.001151768
## GO:1902554 3/20 136/19894 3.271542e-04 0.010135391 0.005391776
## GO:0016514 2/20 30/19894 4.106920e-04 0.010135391 0.005391776
## GO:1902911 3/20 150/19894 4.359308e-04 0.010135391 0.005391776
## GO:0005925 4/20 421/19894 7.320323e-04 0.012387254 0.006589711
## GO:0030055 4/20 431/19894 7.991777e-04 0.012387254 0.006589711
## geneID Count
## GO:0000307 RB1/CCND1/CDKN1A 3
## GO:1902554 RB1/CCND1/CDKN1A 3
## GO:0016514 RB1/ARID1A 2
## GO:1902911 RB1/CCND1/CDKN1A 3
## GO:0005925 KRAS/PTK2/YWHAZ/ITGA2 4
## GO:0030055 KRAS/PTK2/YWHAZ/ITGA2 4
## ID Description GeneRatio
## GO:0008190 GO:0008190 eukaryotic initiation factor 4E binding 2/35
## GO:0003684 GO:0003684 damaged DNA binding 3/35
## GO:0019887 GO:0019887 protein kinase regulator activity 4/35
## GO:0001221 GO:0001221 transcription coregulator binding 3/35
## GO:0019207 GO:0019207 kinase regulator activity 4/35
## GO:0031369 GO:0031369 translation initiation factor binding 2/35
## BgRatio pvalue p.adjust qvalue geneID
## GO:0008190 10/18522 0.0001546248 0.03741919 0.02164747 EIF4EBP1/EIF4G1
## GO:0003684 73/18522 0.0003511289 0.04248659 0.02457902 XRCC5/TP63/PARP1
## GO:0019887 232/18522 0.0009258617 0.04890590 0.02829267 ERBB3/CCNB1/YWHAB/CCNE2
## GO:0001221 114/18522 0.0012875289 0.04890590 0.02829267 GATA3/AR/EZH2
## GO:0019207 270/18522 0.0016203361 0.04890590 0.02829267 ERBB3/CCNB1/YWHAB/CCNE2
## GO:0031369 32/18522 0.0016604070 0.04890590 0.02829267 EIF4EBP1/EIF4G1
## Count
## GO:0008190 2
## GO:0003684 3
## GO:0019887 4
## GO:0001221 3
## GO:0019207 4
## GO:0031369 2
## ID Description
## GO:0045931 GO:0045931 positive regulation of mitotic cell cycle
## GO:0032200 GO:0032200 telomere organization
## GO:0045859 GO:0045859 regulation of protein kinase activity
## GO:0045787 GO:0045787 positive regulation of cell cycle
## GO:1901989 GO:1901989 positive regulation of cell cycle phase transition
## GO:1902298 GO:1902298 cell cycle DNA replication maintenance of fidelity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0045931 6/36 130/18888 1.556436e-07 0.0003052171 0.0001720272
## GO:0032200 6/36 189/18888 1.406881e-06 0.0007847751 0.0004423167
## GO:0045859 8/36 470/18888 2.271196e-06 0.0007847751 0.0004423167
## GO:0045787 7/36 332/18888 2.621030e-06 0.0007847751 0.0004423167
## GO:1901989 5/36 117/18888 2.706115e-06 0.0007847751 0.0004423167
## GO:1902298 2/36 2/18888 3.532007e-06 0.0007847751 0.0004423167
## geneID Count
## GO:0045931 EIF4EBP1/EIF4G1/BRCA2/CDK1/CCNB1/CCNE2 6
## GO:0032200 RAD51/XRCC5/BRCA2/EZH2/CCNE2/PARP1 6
## GO:0045859 XRCC5/ADAR/PDCD4/PTK2/CCNB1/EZH2/CCNE2/ERRFI1 8
## GO:0045787 EIF4EBP1/EIF4G1/BRCA2/CDK1/CCNB1/EZH2/CCNE2 7
## GO:1901989 EIF4G1/CDK1/CCNB1/EZH2/CCNE2 5
## GO:1902298 RAD51/BRCA2 2
## ID Description
## GO:0000781 GO:0000781 chromosome, telomeric region
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex
## GO:0098687 GO:0098687 chromosomal region
## GO:1902554 GO:1902554 serine/threonine protein kinase complex
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:1902911 GO:1902911 protein kinase complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0000781 6/36 173/19894 6.219983e-07 0.0001156917 6.940191e-05
## GO:0097125 2/36 2/19894 3.183817e-06 0.0002960950 1.776235e-04
## GO:0098687 7/36 402/19894 6.571942e-06 0.0004074604 2.444301e-04
## GO:1902554 4/36 136/19894 1.038614e-04 0.0046992349 2.819009e-03
## GO:0000307 3/36 56/19894 1.412264e-04 0.0046992349 2.819009e-03
## GO:1902911 4/36 150/19894 1.515882e-04 0.0046992349 2.819009e-03
## geneID Count
## GO:0000781 RAD51/XRCC5/BRCA2/CDK1/EZH2/PARP1 6
## GO:0097125 CDK1/CCNB1 2
## GO:0098687 RAD51/XRCC5/BRCA2/CDK1/CCNB1/EZH2/PARP1 7
## GO:1902554 XRCC5/CDK1/CCNB1/CCNE2 4
## GO:0000307 CDK1/CCNB1/CCNE2 3
## GO:1902911 XRCC5/CDK1/CCNB1/CCNE2 4
## ID Description GeneRatio
## GO:0032143 GO:0032143 single thymine insertion binding 2/30
## GO:0035173 GO:0035173 histone kinase activity 3/30
## GO:0032137 GO:0032137 guanine/thymine mispair binding 2/30
## GO:0032142 GO:0032142 single guanine insertion binding 2/30
## GO:0032138 GO:0032138 single base insertion or deletion binding 2/30
## GO:0032135 GO:0032135 DNA insertion or deletion binding 2/30
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0032143 2/18522 2.536103e-06 0.0004180353 0.0002000169 MSH6/MSH2 2
## GO:0035173 23/18522 6.643582e-06 0.0004180353 0.0002000169 PRKCA/CDK1/ATM 3
## GO:0032137 3/18522 7.600641e-06 0.0004180353 0.0002000169 MSH6/MSH2 2
## GO:0032142 3/18522 7.600641e-06 0.0004180353 0.0002000169 MSH6/MSH2 2
## GO:0032138 4/18522 1.518596e-05 0.0006681823 0.0003197045 MSH6/MSH2 2
## GO:0032135 6/18522 3.788843e-05 0.0011907792 0.0005697508 MSH6/MSH2 2
## ID
## GO:0010165 GO:0010165
## GO:0002520 GO:0002520
## GO:0045785 GO:0045785
## GO:0002285 GO:0002285
## GO:0051053 GO:0051053
## GO:0002562 GO:0002562
## Description
## GO:0010165 response to X-ray
## GO:0002520 immune system development
## GO:0045785 positive regulation of cell adhesion
## GO:0002285 lymphocyte activation involved in immune response
## GO:0051053 negative regulation of DNA metabolic process
## GO:0002562 somatic diversification of immune receptors via germline recombination within a single locus
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010165 4/30 28/18888 1.030795e-07 0.0001804922 9.613521e-05
## GO:0002520 6/30 197/18888 5.749726e-07 0.0003706617 1.974248e-04
## GO:0045785 8/30 485/18888 6.350572e-07 0.0003706617 1.974248e-04
## GO:0002285 6/30 212/18888 8.833118e-07 0.0003866698 2.059511e-04
## GO:0051053 5/30 142/18888 2.741088e-06 0.0009599292 5.112851e-04
## GO:0002562 4/30 70/18888 4.407252e-06 0.0011024427 5.871918e-04
## geneID Count
## GO:0010165 GATA3/ATM/BRCA2/MSH2 4
## GO:0002520 RBM15/GATA3/ATM/MSH6/TFRC/MSH2 6
## GO:0045785 PRKCA/IGFBP2/GATA3/ATM/TSC1/XBP1/TFRC/PREX1 8
## GO:0002285 GATA3/TSC1/XBP1/MSH6/TFRC/MSH2 6
## GO:0051053 GATA3/ATM/TTF1/MSH6/MSH2 5
## GO:0002562 ATM/MSH6/TFRC/MSH2 4
## ID Description GeneRatio BgRatio
## GO:0042470 GO:0042470 melanosome 5/30 112/19894
## GO:0048770 GO:0048770 pigment granule 5/30 112/19894
## GO:0032301 GO:0032301 MutSalpha complex 2/30 2/19894
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex 2/30 2/19894
## GO:0032300 GO:0032300 mismatch repair complex 2/30 11/19894
## GO:0000781 GO:0000781 chromosome, telomeric region 4/30 173/19894
## pvalue p.adjust qvalue geneID
## GO:0042470 6.584008e-07 4.016245e-05 2.772214e-05 FASN/YWHAB/PRDX1/MYH11/TFRC
## GO:0048770 6.584008e-07 4.016245e-05 2.772214e-05 FASN/YWHAB/PRDX1/MYH11/TFRC
## GO:0032301 2.198350e-06 6.704968e-05 4.628105e-05 MSH6/MSH2
## GO:0097125 2.198350e-06 6.704968e-05 4.628105e-05 CDK1/CCNB1
## GO:0032300 1.198923e-04 2.579428e-03 1.780451e-03 MSH6/MSH2
## GO:0000781 1.268571e-04 2.579428e-03 1.780451e-03 CDK1/ATM/BRCA2/MSH2
## Count
## GO:0042470 5
## GO:0048770 5
## GO:0032301 2
## GO:0097125 2
## GO:0032300 2
## GO:0000781 4
## ID Description GeneRatio
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 2/23
## GO:0106310 GO:0106310 protein serine kinase activity 5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 5/23
## GO:0004707 GO:0004707 MAP kinase activity 2/23
## GO:0070064 GO:0070064 proline-rich region binding 2/23
## GO:0042826 GO:0042826 histone deacetylase binding 3/23
## BgRatio pvalue p.adjust qvalue
## GO:0120283 7/18522 3.085855e-05 0.005523681 0.002273788
## GO:0106310 363/18522 7.075911e-05 0.006332941 0.002606915
## GO:0004674 427/18522 1.518718e-04 0.007100610 0.002922921
## GO:0004707 16/18522 1.751391e-04 0.007100610 0.002922921
## GO:0070064 17/18522 1.983411e-04 0.007100610 0.002922921
## GO:0042826 128/18522 5.160029e-04 0.015394085 0.006336877
## geneID Count
## GO:0120283 MAPK8/XIAP 2
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004707 MAPK8/MAPK1 2
## GO:0070064 CCND1/YAP1 2
## GO:0042826 HSPA1A/MAPK8/CCND1 3
## ID Description GeneRatio
## GO:0010631 GO:0010631 epithelial cell migration 9/23
## GO:0090132 GO:0090132 epithelium migration 9/23
## GO:0090130 GO:0090130 tissue migration 9/23
## GO:0001667 GO:0001667 ameboidal-type cell migration 9/23
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus 8/23
## BgRatio pvalue p.adjust qvalue
## GO:0010631 375/18888 2.784961e-10 2.143530e-07 8.314100e-08
## GO:0090132 378/18888 2.988249e-10 2.143530e-07 8.314100e-08
## GO:0090130 383/18888 3.356258e-10 2.143530e-07 8.314100e-08
## GO:0001667 498/18888 3.370825e-09 1.092718e-06 4.238319e-07
## GO:0071214 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## GO:0104004 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 6/23 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 6/23 431/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/23 4/19894
## GO:0070938 GO:0070938 contractile ring 2/23 10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 4/23 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 4/23 248/19894
## pvalue p.adjust qvalue
## GO:0005925 6.447048e-06 0.0003166418 0.0001720295
## GO:0030055 7.373490e-06 0.0003166418 0.0001720295
## GO:0005826 7.660689e-06 0.0003166418 0.0001720295
## GO:0070938 5.721303e-05 0.0017736039 0.0009635879
## GO:0005741 1.073470e-04 0.0026622052 0.0014463593
## GO:0031968 1.732117e-04 0.0031642699 0.0017191279
## geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1 6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1 6
## GO:0005826 MYH9/ANLN 2
## GO:0070938 MYH9/ANLN 2
## GO:0005741 MTOR/FOXO3/CASP8/KRAS 4
## GO:0031968 MTOR/FOXO3/CASP8/KRAS 4
## ID
## GO:0120283 GO:0120283
## GO:0140297 GO:0140297
## GO:0031625 GO:0031625
## GO:0044389 GO:0044389
## GO:0061629 GO:0061629
## GO:0140311 GO:0140311
## Description
## GO:0120283 protein serine/threonine kinase binding
## GO:0140297 DNA-binding transcription factor binding
## GO:0031625 ubiquitin protein ligase binding
## GO:0044389 ubiquitin-like protein ligase binding
## GO:0061629 RNA polymerase II-specific DNA-binding transcription factor binding
## GO:0140311 protein sequestering activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0120283 2/17 7/18522 1.660593e-05 0.002358042 0.0008914761
## GO:0140297 5/17 478/18522 5.365384e-05 0.003809423 0.0014401820
## GO:0031625 4/17 305/18522 1.448503e-04 0.006454095 0.0024400209
## GO:0044389 4/17 324/18522 1.827003e-04 0.006454095 0.0024400209
## GO:0061629 4/17 343/18522 2.272569e-04 0.006454095 0.0024400209
## GO:0140311 2/17 29/18522 3.172573e-04 0.007508423 0.0028386181
## geneID Count
## GO:0120283 XIAP/MAPK8 2
## GO:0140297 RB1/ETS1/ARID1A/YWHAZ/NCOA3 5
## GO:0031625 RB1/BID/YWHAZ/CDKN1A 4
## GO:0044389 RB1/BID/YWHAZ/CDKN1A 4
## GO:0061629 RB1/ETS1/ARID1A/NCOA3 4
## GO:0140311 YWHAZ/CDKN1A 2
## ID
## GO:2000045 GO:2000045
## GO:1902806 GO:1902806
## GO:0000082 GO:0000082
## GO:0044843 GO:0044843
## GO:2000134 GO:2000134
## GO:1901990 GO:1901990
## Description
## GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 regulation of cell cycle G1/S phase transition
## GO:0000082 G1/S transition of mitotic cell cycle
## GO:0044843 cell cycle G1/S phase transition
## GO:2000134 negative regulation of G1/S transition of mitotic cell cycle
## GO:1901990 regulation of mitotic cell cycle phase transition
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:2000045 7/17 185/18888 1.381696e-10 1.692577e-07 7.359348e-08
## GO:1902806 7/17 211/18888 3.476363e-10 2.129273e-07 9.258105e-08
## GO:0000082 7/17 234/18888 7.166752e-10 2.926424e-07 1.272413e-07
## GO:0044843 7/17 262/18888 1.575684e-09 4.825534e-07 2.098148e-07
## GO:2000134 5/17 85/18888 9.716264e-09 2.380485e-06 1.035038e-06
## GO:1901990 7/17 356/18888 1.317298e-08 2.689483e-06 1.169391e-06
## geneID Count
## GO:2000045 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 7
## GO:1902806 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 7
## GO:0000082 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 7
## GO:0044843 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 7
## GO:2000134 RB1/PTEN/ATM/CCND1/CDKN1A 5
## GO:1901990 RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 7
## ID Description
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:1902554 GO:1902554 serine/threonine protein kinase complex
## GO:1902911 GO:1902911 protein kinase complex
## GO:0016514 GO:0016514 SWI/SNF complex
## GO:0005925 GO:0005925 focal adhesion
## GO:0030055 GO:0030055 cell-substrate junction
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0000307 3/17 56/19894 1.397003e-05 0.001117602 0.0005735065
## GO:1902554 3/17 136/19894 1.980967e-04 0.005510756 0.0028278880
## GO:1902911 3/17 150/19894 2.643788e-04 0.005510756 0.0028278880
## GO:0016514 2/17 30/19894 2.947971e-04 0.005510756 0.0028278880
## GO:0005925 4/17 421/19894 3.781266e-04 0.005510756 0.0028278880
## GO:0030055 4/17 431/19894 4.133067e-04 0.005510756 0.0028278880
## geneID Count
## GO:0000307 RB1/CCND1/CDKN1A 3
## GO:1902554 RB1/CCND1/CDKN1A 3
## GO:1902911 RB1/CCND1/CDKN1A 3
## GO:0016514 RB1/ARID1A 2
## GO:0005925 KRAS/PTK2/YWHAZ/ITGA2 4
## GO:0030055 KRAS/PTK2/YWHAZ/ITGA2 4
## ID Description GeneRatio
## GO:0045296 GO:0045296 cadherin binding 12/62
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 12/62
## GO:0019903 GO:0019903 protein phosphatase binding 7/62
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 9/62
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 9/62
## GO:0019902 GO:0019902 phosphatase binding 7/62
## BgRatio pvalue p.adjust qvalue
## GO:0045296 333/18522 9.037285e-10 3.533578e-07 1.702815e-07
## GO:0140297 478/18522 5.094827e-08 9.960387e-06 4.799863e-06
## GO:0019903 142/18522 4.640913e-07 6.048657e-05 2.914819e-05
## GO:0031625 305/18522 7.466285e-07 7.298293e-05 3.517013e-05
## GO:0044389 324/18522 1.232957e-06 9.641722e-05 4.646300e-05
## GO:0019902 189/18522 3.155486e-06 2.056325e-04 9.909334e-05
## geneID
## GO:0045296 EGFR/CDH1/MYH9/YWHAZ/NDRG1/CTNNA1/PRDX1/YWHAB/NOTCH3/EEF2/VASP/FASN
## GO:0140297 SMAD4/RB1/E2F1/MYC/YWHAZ/NCOA3/PARP1/JUN/TP53/STAT3/ARID1A/VHL
## GO:0019903 EGFR/MET/MAPK8/CDKN1B/PXN/TP53/STAT3
## GO:0031625 EGFR/TUBA1B/RB1/YWHAZ/CASP8/PARP1/CDKN1B/JUN/TP53
## GO:0044389 EGFR/TUBA1B/RB1/YWHAZ/CASP8/PARP1/CDKN1B/JUN/TP53
## GO:0019902 EGFR/MET/MAPK8/CDKN1B/PXN/TP53/STAT3
## Count
## GO:0045296 12
## GO:0140297 12
## GO:0019903 7
## GO:0031625 9
## GO:0044389 9
## GO:0019902 7
## ID Description GeneRatio BgRatio
## GO:0062197 GO:0062197 cellular response to chemical stress 15/62 311/18888
## GO:0051402 GO:0051402 neuron apoptotic process 14/62 292/18888
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle 13/62 234/18888
## GO:0034599 GO:0034599 cellular response to oxidative stress 13/62 248/18888
## GO:0097305 GO:0097305 response to alcohol 13/62 259/18888
## GO:0044843 GO:0044843 cell cycle G1/S phase transition 13/62 262/18888
## pvalue p.adjust qvalue
## GO:0062197 5.868369e-14 1.839734e-10 7.993337e-11
## GO:0051402 4.880667e-13 5.885847e-10 2.557303e-10
## GO:0000082 5.632390e-13 5.885847e-10 2.557303e-10
## GO:0034599 1.181483e-12 9.259874e-10 4.023261e-10
## GO:0097305 2.050313e-12 1.181391e-09 5.132948e-10
## GO:0044843 2.372544e-12 1.181391e-09 5.132948e-10
## geneID
## GO:0062197 EGFR/MET/AKT1/CASP3/ATM/MAPK8/PARP1/MTOR/PRDX1/PRKAA1/PXN/JUN/TP53/G6PD/CDK1
## GO:0051402 BCL2L1/CASP3/ATM/XIAP/RB1/CASP8/PARP1/BCL2L11/TP53/AKT2/GAPDH/AKT1S1/G6PD/MSH2
## GO:0000082 EGFR/AKT1/ATM/RB1/E2F1/MYC/EIF4EBP1/CDKN1B/TP53/EIF4G1/ARID1A/PTEN/CDK1
## GO:0034599 EGFR/MET/AKT1/ATM/MAPK8/PARP1/PRDX1/PRKAA1/PXN/JUN/TP53/G6PD/CDK1
## GO:0097305 AKT1/BCL2L1/IGF1R/CDH1/CASP8/RAD51/PARP1/CTNNA1/PRKAA1/EIF4G1/PTCH1/G6PD/CDK1
## GO:0044843 EGFR/AKT1/ATM/RB1/E2F1/MYC/EIF4EBP1/CDKN1B/TP53/EIF4G1/ARID1A/PTEN/CDK1
## Count
## GO:0062197 15
## GO:0051402 14
## GO:0000082 13
## GO:0034599 13
## GO:0097305 13
## GO:0044843 13
## ID Description
## GO:0031252 GO:0031252 cell leading edge
## GO:0030027 GO:0030027 lamellipodium
## GO:0005901 GO:0005901 caveola
## GO:0038201 GO:0038201 TOR complex
## GO:0090575 GO:0090575 RNA polymerase II transcription regulator complex
## GO:0016605 GO:0016605 PML body
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0031252 11/62 426/19894 7.269174e-08 1.744602e-05 8.799526e-06
## GO:0030027 7/62 203/19894 3.176241e-06 3.729449e-04 1.881082e-04
## GO:0005901 5/62 82/19894 5.659915e-06 3.729449e-04 1.881082e-04
## GO:0038201 3/62 12/19894 6.215748e-06 3.729449e-04 1.881082e-04
## GO:0090575 7/62 255/19894 1.411896e-05 6.777100e-04 3.418274e-04
## GO:0016605 5/62 108/19894 2.173211e-05 7.211011e-04 3.637133e-04
## geneID Count
## GO:0031252 EGFR/AKT1/CDH1/NF2/MYH9/CASP8/CTNNA1/PXN/ERBB2/AKT2/VASP 11
## GO:0030027 AKT1/CDH1/NF2/CASP8/CTNNA1/PXN/VASP 7
## GO:0005901 IGF1R/CDH1/CTNNA1/PTCH1/IRS1 5
## GO:0038201 MTOR/AKT1S1/RICTOR 3
## GO:0090575 SMAD4/RB1/E2F1/MYC/JUN/XBP1/STAT3 7
## GO:0016605 RB1/RAD51/MTOR/TP53/PTEN 5
## ID Description GeneRatio
## GO:0003684 GO:0003684 damaged DNA binding 4/35
## GO:0043125 GO:0043125 ErbB-3 class receptor binding 2/35
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding 3/35
## GO:0004707 GO:0004707 MAP kinase activity 2/35
## GO:0019902 GO:0019902 phosphatase binding 4/35
## GO:0051219 GO:0051219 phosphoprotein binding 3/35
## BgRatio pvalue p.adjust qvalue
## GO:0003684 73/18522 1.059881e-05 0.002458925 0.001383424
## GO:0043125 5/18522 3.456577e-05 0.004009629 0.002255871
## GO:0045309 59/18522 1.868833e-04 0.014452308 0.008131062
## GO:0004707 16/18522 4.094059e-04 0.019921948 0.011208355
## GO:0019902 189/18522 4.293523e-04 0.019921948 0.011208355
## GO:0051219 93/18522 7.139065e-04 0.027604384 0.015530597
## geneID Count
## GO:0003684 XRCC5/TP63/ERCC1/PARP1 4
## GO:0043125 ERBB3/NRG1 2
## GO:0045309 MAPK1/LCK/YWHAB 3
## GO:0004707 MAPK14/MAPK1 2
## GO:0019902 MAPK14/MAPK1/PTK2/LCK 4
## GO:0051219 MAPK1/LCK/YWHAB 3
## ID Description GeneRatio
## GO:0071478 GO:0071478 cellular response to radiation 8/36
## GO:0010212 GO:0010212 response to ionizing radiation 7/36
## GO:0061180 GO:0061180 mammary gland epithelium development 5/36
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 8/36
## GO:0104004 GO:0104004 cellular response to environmental stimulus 8/36
## GO:0030879 GO:0030879 mammary gland development 6/36
## BgRatio pvalue p.adjust qvalue
## GO:0071478 181/18888 1.465387e-09 3.001113e-06 1.613468e-06
## GO:0010212 138/18888 6.669773e-09 6.829848e-06 3.671886e-06
## GO:0061180 67/18888 1.670382e-07 5.637465e-05 3.030833e-05
## GO:0071214 334/18888 1.728301e-07 5.637465e-05 3.030833e-05
## GO:0104004 334/18888 1.728301e-07 5.637465e-05 3.030833e-05
## GO:0030879 135/18888 1.947229e-07 5.637465e-05 3.030833e-05
## geneID Count
## GO:0071478 MAPK14/AKT2/RAD51/GATA3/XRCC5/BRCA2/ERCC1/PARP1 8
## GO:0010212 MAPK14/RAD51/GATA3/XRCC5/BRCA2/ERCC1/PARP1 7
## GO:0061180 AKT2/GATA3/MAPK1/BRCA2/AR 5
## GO:0071214 MAPK14/AKT2/RAD51/GATA3/XRCC5/BRCA2/ERCC1/PARP1 8
## GO:0104004 MAPK14/AKT2/RAD51/GATA3/XRCC5/BRCA2/ERCC1/PARP1 8
## GO:0030879 AKT2/GATA3/MAPK1/BRCA2/AR/NRG1 6
## ID Description GeneRatio BgRatio
## GO:0000781 GO:0000781 chromosome, telomeric region 5/36 173/19894
## GO:0000800 GO:0000800 lateral element 2/36 14/19894
## GO:0031143 GO:0031143 pseudopodium 2/36 18/19894
## GO:1990391 GO:1990391 DNA repair complex 2/36 22/19894
## GO:0098687 GO:0098687 chromosomal region 5/36 402/19894
## GO:0090734 GO:0090734 site of DNA damage 3/36 123/19894
## pvalue p.adjust qvalue geneID
## GO:0000781 1.422251e-05 0.002474716 0.001527048 RAD51/XRCC5/BRCA2/ERCC1/PARP1
## GO:0000800 2.857927e-04 0.024863964 0.015342555 RAD51/BRCA2
## GO:0031143 4.783253e-04 0.025735885 0.015880583 MAPK1/RAB25
## GO:1990391 7.188974e-04 0.025735885 0.015880583 XRCC5/BRCA2
## GO:0098687 7.395369e-04 0.025735885 0.015880583 RAD51/XRCC5/BRCA2/ERCC1/PARP1
## GO:0090734 1.418836e-03 0.041146250 0.025389701 RAD51/XRCC5/PARP1
## Count
## GO:0000781 5
## GO:0000800 2
## GO:0031143 2
## GO:1990391 2
## GO:0098687 5
## GO:0090734 3
## ID Description GeneRatio
## GO:0032143 GO:0032143 single thymine insertion binding 2/27
## GO:0035173 GO:0035173 histone kinase activity 3/27
## GO:0032137 GO:0032137 guanine/thymine mispair binding 2/27
## GO:0032142 GO:0032142 single guanine insertion binding 2/27
## GO:0032138 GO:0032138 single base insertion or deletion binding 2/27
## GO:0032135 GO:0032135 DNA insertion or deletion binding 2/27
## BgRatio pvalue p.adjust qvalue geneID Count
## GO:0032143 2/18522 2.046373e-06 0.0003005461 0.0001371988 MSH6/MSH2 2
## GO:0035173 23/18522 4.797970e-06 0.0003005461 0.0001371988 PRKCA/CDK1/ATM 3
## GO:0032137 3/18522 6.133594e-06 0.0003005461 0.0001371988 MSH6/MSH2 2
## GO:0032142 3/18522 6.133594e-06 0.0003005461 0.0001371988 MSH6/MSH2 2
## GO:0032138 4/18522 1.225615e-05 0.0004804411 0.0002193206 MSH6/MSH2 2
## GO:0032135 6/18522 3.058526e-05 0.0008563873 0.0003909394 MSH6/MSH2 2
## ID Description
## GO:0010165 GO:0010165 response to X-ray
## GO:0045785 GO:0045785 positive regulation of cell adhesion
## GO:0002520 GO:0002520 immune system development
## GO:0002285 GO:0002285 lymphocyte activation involved in immune response
## GO:0045931 GO:0045931 positive regulation of mitotic cell cycle
## GO:0051053 GO:0051053 negative regulation of DNA metabolic process
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0010165 4/27 28/18888 6.621328e-08 0.0001052791 5.429489e-05
## GO:0045785 8/27 485/18888 2.577809e-07 0.0001559259 8.041462e-05
## GO:0002520 6/27 197/18888 2.941998e-07 0.0001559259 8.041462e-05
## GO:0002285 6/27 212/18888 4.528952e-07 0.0001800258 9.284351e-05
## GO:0045931 5/27 130/18888 1.022030e-06 0.0003250055 1.676129e-04
## GO:0051053 5/27 142/18888 1.581256e-06 0.0004190327 2.161049e-04
## geneID Count
## GO:0010165 GATA3/ATM/BRCA2/MSH2 4
## GO:0045785 PRKCA/PREX1/IGFBP2/GATA3/ATM/TSC1/XBP1/TFRC 8
## GO:0002520 MSH6/RBM15/GATA3/ATM/TFRC/MSH2 6
## GO:0002285 MSH6/GATA3/TSC1/XBP1/TFRC/MSH2 6
## GO:0045931 PRKCA/CDK1/CCNB1/ASNS/BRCA2 5
## GO:0051053 MSH6/GATA3/ATM/TTF1/MSH2 5
## ID Description GeneRatio BgRatio
## GO:0032301 GO:0032301 MutSalpha complex 2/27 2/19894
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex 2/27 2/19894
## GO:0042470 GO:0042470 melanosome 4/27 112/19894
## GO:0048770 GO:0048770 pigment granule 4/27 112/19894
## GO:0000781 GO:0000781 chromosome, telomeric region 4/27 173/19894
## GO:0032300 GO:0032300 mismatch repair complex 2/27 11/19894
## pvalue p.adjust qvalue geneID Count
## GO:0032301 1.773841e-06 0.0001011089 7.655525e-05 MSH6/MSH2 2
## GO:0097125 1.773841e-06 0.0001011089 7.655525e-05 CDK1/CCNB1 2
## GO:0042470 1.511691e-05 0.0004308319 3.262069e-04 FASN/PRDX1/MYH11/TFRC 4
## GO:0048770 1.511691e-05 0.0004308319 3.262069e-04 FASN/PRDX1/MYH11/TFRC 4
## GO:0000781 8.290780e-05 0.0018397365 1.392968e-03 CDK1/ATM/BRCA2/MSH2 4
## GO:0032300 9.682824e-05 0.0018397365 1.392968e-03 MSH6/MSH2 2
## ID Description GeneRatio
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 2/23
## GO:0106310 GO:0106310 protein serine kinase activity 5/23
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 5/23
## GO:0004707 GO:0004707 MAP kinase activity 2/23
## GO:0070064 GO:0070064 proline-rich region binding 2/23
## GO:0042826 GO:0042826 histone deacetylase binding 3/23
## BgRatio pvalue p.adjust qvalue
## GO:0120283 7/18522 3.085855e-05 0.005523681 0.002273788
## GO:0106310 363/18522 7.075911e-05 0.006332941 0.002606915
## GO:0004674 427/18522 1.518718e-04 0.007100610 0.002922921
## GO:0004707 16/18522 1.751391e-04 0.007100610 0.002922921
## GO:0070064 17/18522 1.983411e-04 0.007100610 0.002922921
## GO:0042826 128/18522 5.160029e-04 0.015394085 0.006336877
## geneID Count
## GO:0120283 MAPK8/XIAP 2
## GO:0106310 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004674 AKT1/MTOR/MAPK8/ATM/MAPK1 5
## GO:0004707 MAPK8/MAPK1 2
## GO:0070064 CCND1/YAP1 2
## GO:0042826 HSPA1A/MAPK8/CCND1 3
## ID Description GeneRatio
## GO:0010631 GO:0010631 epithelial cell migration 9/23
## GO:0090132 GO:0090132 epithelium migration 9/23
## GO:0090130 GO:0090130 tissue migration 9/23
## GO:0001667 GO:0001667 ameboidal-type cell migration 9/23
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 8/23
## GO:0104004 GO:0104004 cellular response to environmental stimulus 8/23
## BgRatio pvalue p.adjust qvalue
## GO:0010631 375/18888 2.784961e-10 2.143530e-07 8.314100e-08
## GO:0090132 378/18888 2.988249e-10 2.143530e-07 8.314100e-08
## GO:0090130 383/18888 3.356258e-10 2.143530e-07 8.314100e-08
## GO:0001667 498/18888 3.370825e-09 1.092718e-06 4.238319e-07
## GO:0071214 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## GO:0104004 334/18888 3.421872e-09 1.092718e-06 4.238319e-07
## geneID Count
## GO:0010631 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090132 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0090130 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0001667 AKT1/MTOR/MYH9/PTEN/PTK2/ETS1/STAT5A/ITGA2/ANLN 9
## GO:0071214 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## GO:0104004 MTOR/MAPK8/CDKN1A/ATM/CASP8/PTEN/YAP1/ITGA2 8
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 6/23 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 6/23 431/19894
## GO:0005826 GO:0005826 actomyosin contractile ring 2/23 4/19894
## GO:0070938 GO:0070938 contractile ring 2/23 10/19894
## GO:0005741 GO:0005741 mitochondrial outer membrane 4/23 219/19894
## GO:0031968 GO:0031968 organelle outer membrane 4/23 248/19894
## pvalue p.adjust qvalue
## GO:0005925 6.447048e-06 0.0003166418 0.0001720295
## GO:0030055 7.373490e-06 0.0003166418 0.0001720295
## GO:0005826 7.660689e-06 0.0003166418 0.0001720295
## GO:0070938 5.721303e-05 0.0017736039 0.0009635879
## GO:0005741 1.073470e-04 0.0026622052 0.0014463593
## GO:0031968 1.732117e-04 0.0031642699 0.0017191279
## geneID Count
## GO:0005925 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1 6
## GO:0030055 HSPA1A/MYH9/KRAS/PTK2/ITGA2/MAPK1 6
## GO:0005826 MYH9/ANLN 2
## GO:0070938 MYH9/ANLN 2
## GO:0005741 MTOR/FOXO3/CASP8/KRAS 4
## GO:0031968 MTOR/FOXO3/CASP8/KRAS 4
## ID
## GO:0003684 GO:0003684
## GO:0032139 GO:0032139
## GO:1990599 GO:1990599
## GO:0106017 GO:0106017
## GO:0032135 GO:0032135
## GO:0032405 GO:0032405
## Description
## GO:0003684 damaged DNA binding
## GO:0032139 dinucleotide insertion or deletion binding
## GO:1990599 3' overhang single-stranded DNA endodeoxyribonuclease activity
## GO:0106017 phosphatidylinositol-3,4-bisphosphate phosphatase activity
## GO:0032135 DNA insertion or deletion binding
## GO:0032405 MutLalpha complex binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0003684 4/27 73/18522 3.638183e-06 0.0004763758 0.0001915403
## GO:0032139 2/27 3/18522 6.133594e-06 0.0004763758 0.0001915403
## GO:1990599 2/27 3/18522 6.133594e-06 0.0004763758 0.0001915403
## GO:0106017 2/27 4/18522 1.225615e-05 0.0007139207 0.0002870519
## GO:0032135 2/27 6/18522 3.058526e-05 0.0011877276 0.0004775593
## GO:0032405 2/27 6/18522 3.058526e-05 0.0011877276 0.0004775593
## geneID Count
## GO:0003684 PCNA/XRCC1/ERCC1/MSH2 4
## GO:0032139 PCNA/MSH2 2
## GO:1990599 XRCC1/ERCC1 2
## GO:0106017 PTEN/INPP4B 2
## GO:0032135 PCNA/MSH2 2
## GO:0032405 PCNA/MSH2 2
## ID Description GeneRatio
## GO:0010165 GO:0010165 response to X-ray 5/27
## GO:0051054 GO:0051054 positive regulation of DNA metabolic process 8/27
## GO:0006312 GO:0006312 mitotic recombination 4/27
## GO:0006979 GO:0006979 response to oxidative stress 8/27
## GO:0048732 GO:0048732 gland development 8/27
## GO:1904354 GO:1904354 negative regulation of telomere capping 3/27
## BgRatio pvalue p.adjust qvalue
## GO:0010165 28/18888 3.875046e-10 7.606715e-07 3.491620e-07
## GO:0051054 301/18888 6.468898e-09 6.349223e-06 2.914409e-06
## GO:0006312 25/18888 4.102815e-08 2.684608e-05 1.232284e-05
## GO:0006979 398/18888 5.664809e-08 2.780005e-05 1.276073e-05
## GO:0048732 449/18888 1.430479e-07 4.749793e-05 2.180241e-05
## GO:1904354 8/18888 1.451796e-07 4.749793e-05 2.180241e-05
## geneID Count
## GO:0010165 GATA3/ATM/BRCA2/ERCC1/MSH2 5
## GO:0051054 ATM/EGFR/PCNA/CDK1/XRCC1/ERCC1/TFRC/MSH2 8
## GO:0006312 BRCA2/XRCC1/ERCC1/MSH2 4
## GO:0006979 G6PD/ATM/EGFR/PCNA/CDK1/XRCC1/PRDX1/ERCC1 8
## GO:0048732 GATA3/ATM/BRCA2/EGFR/FASN/PCNA/AR/XBP1 8
## GO:1904354 ATM/XRCC1/ERCC1 3
## ID Description GeneRatio BgRatio
## GO:0000781 GO:0000781 chromosome, telomeric region 7/27 173/19894
## GO:0098687 GO:0098687 chromosomal region 7/27 402/19894
## GO:0070522 GO:0070522 ERCC4-ERCC1 complex 2/27 4/19894
## GO:0000109 GO:0000109 nucleotide-excision repair complex 2/27 12/19894
## GO:1990391 GO:1990391 DNA repair complex 2/27 22/19894
## GO:0042470 GO:0042470 melanosome 3/27 112/19894
## pvalue p.adjust qvalue
## GO:0000781 2.553497e-09 3.319546e-07 2.042797e-07
## GO:0098687 8.178489e-07 5.316018e-05 3.271396e-05
## GO:0070522 1.062522e-05 4.604262e-04 2.833392e-04
## GO:0000109 1.160966e-04 3.773139e-03 2.321932e-03
## GO:1990391 4.029496e-04 8.550575e-03 5.261892e-03
## GO:0042470 4.604156e-04 8.550575e-03 5.261892e-03
## geneID Count
## GO:0000781 ATM/BRCA2/PCNA/CDK1/XRCC1/ERCC1/MSH2 7
## GO:0098687 ATM/BRCA2/PCNA/CDK1/XRCC1/ERCC1/MSH2 7
## GO:0070522 XRCC1/ERCC1 2
## GO:0000109 XRCC1/ERCC1 2
## GO:1990391 ATM/BRCA2 2
## GO:0042470 FASN/PRDX1/TFRC 3
## ID Description GeneRatio
## GO:0140297 GO:0140297 DNA-binding transcription factor binding 7/22
## GO:0051434 GO:0051434 BH3 domain binding 2/22
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 5/22
## GO:0120283 GO:0120283 protein serine/threonine kinase binding 2/22
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 5/22
## GO:0051400 GO:0051400 BH domain binding 2/22
## BgRatio pvalue p.adjust qvalue
## GO:0140297 478/18522 8.892664e-07 0.0001458397 5.616419e-05
## GO:0051434 6/18522 2.014327e-05 0.0010740097 4.136109e-04
## GO:0031625 305/18522 2.451473e-05 0.0010740097 4.136109e-04
## GO:0120283 7/18522 2.818027e-05 0.0010740097 4.136109e-04
## GO:0044389 324/18522 3.274420e-05 0.0010740097 4.136109e-04
## GO:0051400 9/18522 4.823953e-05 0.0013185470 5.077845e-04
## geneID Count
## GO:0140297 BCL2/MYC/RB1/ETS1/ARID1A/YWHAZ/NCOA3 7
## GO:0051434 BCL2/BCL2L1 2
## GO:0031625 BCL2/RB1/BID/YWHAZ/CDKN1A 5
## GO:0120283 XIAP/MAPK8 2
## GO:0044389 BCL2/RB1/BID/YWHAZ/CDKN1A 5
## GO:0051400 BCL2/BCL2L1 2
## ID Description
## GO:0000082 GO:0000082 G1/S transition of mitotic cell cycle
## GO:0044843 GO:0044843 cell cycle G1/S phase transition
## GO:2000045 GO:2000045 regulation of G1/S transition of mitotic cell cycle
## GO:1902806 GO:1902806 regulation of cell cycle G1/S phase transition
## GO:0009314 GO:0009314 response to radiation
## GO:0051402 GO:0051402 neuron apoptotic process
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0000082 10/22 234/18888 3.988594e-14 7.195423e-11 2.594685e-11
## GO:0044843 10/22 262/18888 1.240888e-13 1.119281e-10 4.036150e-11
## GO:2000045 9/22 185/18888 3.041079e-13 1.828702e-10 6.594340e-11
## GO:1902806 9/22 211/18888 1.001594e-12 4.517189e-10 1.628908e-10
## GO:0009314 10/22 431/18888 1.746889e-11 5.593618e-09 2.017071e-09
## GO:0051402 9/22 292/18888 1.860405e-11 5.593618e-09 2.017071e-09
## geneID Count
## GO:0000082 BCL2/MYC/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 10
## GO:0044843 BCL2/MYC/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 10
## GO:2000045 BCL2/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 9
## GO:1902806 BCL2/AKT1/RB1/ARID1A/BID/PTEN/ATM/CCND1/CDKN1A 9
## GO:0009314 AKT2/BCL2/MYC/AKT1/BCL2L1/MAPK8/KRAS/ATM/CCND1/CDKN1A 10
## GO:0051402 AKT2/BCL2/BCL2L1/RB1/XIAP/BID/KRAS/ATM/CCND1 9
## ID Description
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0097136 GO:0097136 Bcl-2 family protein complex
## GO:0005741 GO:0005741 mitochondrial outer membrane
## GO:0031968 GO:0031968 organelle outer membrane
## GO:0019867 GO:0019867 outer membrane
## GO:1902554 GO:1902554 serine/threonine protein kinase complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0000307 3/22 56/19894 3.132362e-05 0.002612600 0.001402554
## GO:0097136 2/22 10/19894 5.225199e-05 0.002612600 0.001402554
## GO:0005741 4/22 219/19894 8.944687e-05 0.002980535 0.001600077
## GO:0031968 4/22 248/19894 1.444963e-04 0.002980535 0.001600077
## GO:0019867 4/22 250/19894 1.490267e-04 0.002980535 0.001600077
## GO:1902554 3/22 136/19894 4.375468e-04 0.007119710 0.003822160
## geneID Count
## GO:0000307 RB1/CCND1/CDKN1A 3
## GO:0097136 BCL2/BCL2L1 2
## GO:0005741 BCL2/BCL2L1/BID/KRAS 4
## GO:0031968 BCL2/BCL2L1/BID/KRAS 4
## GO:0019867 BCL2/BCL2L1/BID/KRAS 4
## GO:1902554 RB1/CCND1/CDKN1A 3
## ID Description
## GO:0004674 GO:0004674 protein serine/threonine kinase activity
## GO:0030544 GO:0030544 Hsp70 protein binding
## GO:0000014 GO:0000014 single-stranded DNA endodeoxyribonuclease activity
## GO:0003684 GO:0003684 damaged DNA binding
## GO:0001618 GO:0001618 virus receptor activity
## GO:0140272 GO:0140272 exogenous protein binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0004674 6/28 427/18522 3.549931e-05 0.007334157 0.003488610
## GO:0030544 3/28 51/18522 6.137370e-05 0.007334157 0.003488610
## GO:0000014 2/28 11/18522 1.201914e-04 0.009366260 0.004455213
## GO:0003684 3/28 73/18522 1.792650e-04 0.009366260 0.004455213
## GO:0001618 3/28 79/18522 2.265476e-04 0.009366260 0.004455213
## GO:0140272 3/28 80/18522 2.351362e-04 0.009366260 0.004455213
## geneID Count
## GO:0004674 MAPK9/EGFR/ACVRL1/EEF2K/ATM/CDK1 6
## GO:0030544 TSC1/CDK1/TFRC 3
## GO:0000014 RAD50/ERCC1 2
## GO:0003684 PARP1/MSH6/ERCC1 3
## GO:0001618 EGFR/CDK1/TFRC 3
## GO:0140272 EGFR/CDK1/TFRC 3
## ID Description GeneRatio
## GO:0045931 GO:0045931 positive regulation of mitotic cell cycle 6/28
## GO:0051053 GO:0051053 negative regulation of DNA metabolic process 6/28
## GO:0006260 GO:0006260 DNA replication 7/28
## GO:1904354 GO:1904354 negative regulation of telomere capping 3/28
## GO:0051054 GO:0051054 positive regulation of DNA metabolic process 7/28
## GO:0032205 GO:0032205 negative regulation of telomere maintenance 4/28
## BgRatio pvalue p.adjust qvalue
## GO:0045931 130/18888 3.149240e-08 4.756438e-05 2.489340e-05
## GO:0051053 142/18888 5.338315e-08 4.756438e-05 2.489340e-05
## GO:0006260 278/18888 1.260997e-07 6.540340e-05 3.422967e-05
## GO:1904354 8/18888 1.625688e-07 6.540340e-05 3.422967e-05
## GO:0051054 301/18888 2.163214e-07 6.540340e-05 3.422967e-05
## GO:0032205 36/18888 2.202135e-07 6.540340e-05 3.422967e-05
## geneID Count
## GO:0045931 EIF4EBP1/EGFR/RAB11A/ASNS/BRCA2/CDK1 6
## GO:0051053 RAD50/PARP1/ATM/TTF1/MSH6/ERCC1 6
## GO:0006260 EGFR/ACVRL1/RAD50/PARP1/BRCA2/TTF1/CDK1 7
## GO:1904354 RAD50/ATM/ERCC1 3
## GO:0051054 EGFR/RAD50/PARP1/ATM/CDK1/ERCC1/TFRC 7
## GO:0032205 RAD50/PARP1/ATM/ERCC1 4
## ID Description GeneRatio BgRatio
## GO:0000781 GO:0000781 chromosome, telomeric region 6/28 173/19894
## GO:0098687 GO:0098687 chromosomal region 6/28 402/19894
## GO:1990391 GO:1990391 DNA repair complex 2/28 22/19894
## GO:0032301 GO:0032301 MutSalpha complex 1/28 2/19894
## GO:0070435 GO:0070435 Shc-EGFR complex 1/28 2/19894
## GO:0097122 GO:0097122 cyclin A2-CDK1 complex 1/28 2/19894
## pvalue p.adjust qvalue
## GO:0000781 1.274426e-07 1.771452e-05 9.658807e-06
## GO:0098687 1.695149e-05 1.178128e-03 6.423722e-04
## GO:1990391 4.336552e-04 2.009269e-02 1.095550e-02
## GO:0032301 2.813009e-03 3.994050e-02 2.177748e-02
## GO:0070435 2.813009e-03 3.994050e-02 2.177748e-02
## GO:0097122 2.813009e-03 3.994050e-02 2.177748e-02
## geneID Count
## GO:0000781 RAD50/PARP1/ATM/BRCA2/CDK1/ERCC1 6
## GO:0098687 RAD50/PARP1/ATM/BRCA2/CDK1/ERCC1 6
## GO:1990391 ATM/BRCA2 2
## GO:0032301 MSH6 1
## GO:0070435 EGFR 1
## GO:0097122 CDK1 1
## ID
## GO:1990599 GO:1990599
## GO:0051219 GO:0051219
## GO:0045296 GO:0045296
## GO:0032356 GO:0032356
## GO:0045309 GO:0045309
## GO:0000014 GO:0000014
## Description
## GO:1990599 3' overhang single-stranded DNA endodeoxyribonuclease activity
## GO:0051219 phosphoprotein binding
## GO:0045296 cadherin binding
## GO:0032356 oxidized DNA binding
## GO:0045309 protein phosphorylated amino acid binding
## GO:0000014 single-stranded DNA endodeoxyribonuclease activity
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:1990599 2/34 3/18522 9.800794e-06 0.002261592 0.001165410
## GO:0051219 4/34 93/18522 2.461113e-05 0.002261592 0.001165410
## GO:0045296 6/34 333/18522 2.838819e-05 0.002261592 0.001165410
## GO:0032356 2/34 10/18522 1.458311e-04 0.006452867 0.003325195
## GO:0045309 3/34 59/18522 1.712518e-04 0.006452867 0.003325195
## GO:0000014 2/34 11/18522 1.780328e-04 0.006452867 0.003325195
## geneID Count
## GO:1990599 XRCC1/ERCC1 2
## GO:0051219 SRC/MAPK1/YWHAE/IRS1 4
## GO:0045296 SRC/VASP/YWHAE/ANLN/RAB11B/EGFR 6
## GO:0032356 XRCC1/MSH6 2
## GO:0045309 MAPK1/YWHAE/IRS1 3
## GO:0000014 XRCC1/ERCC1 2
## ID Description
## GO:0002520 GO:0002520 immune system development
## GO:0031667 GO:0031667 response to nutrient levels
## GO:0031929 GO:0031929 TOR signaling
## GO:0035051 GO:0035051 cardiocyte differentiation
## GO:2000641 GO:2000641 regulation of early endosome to late endosome transport
## GO:0038128 GO:0038128 ERBB2 signaling pathway
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0002520 8/34 197/18888 1.748005e-09 4.006428e-06 1.943046e-06
## GO:0031667 10/34 490/18888 9.448596e-09 8.637050e-06 4.188815e-06
## GO:0031929 7/34 165/18888 1.507339e-08 8.637050e-06 4.188815e-06
## GO:0035051 7/34 165/18888 1.507339e-08 8.637050e-06 4.188815e-06
## GO:2000641 4/34 19/18888 3.326583e-08 1.524906e-05 7.395519e-06
## GO:0038128 4/34 23/18888 7.561261e-08 2.888402e-05 1.400823e-05
## geneID Count
## GO:0002520 MAPK1/MAP2K1/ERCC1/RBM15/GATA3/ATM/MSH6/TFRC 8
## GO:0031667 SRC/MAPK1/ITGA2/TSC1/ERCC1/G6PD/ASNS/EGFR/XBP1/TFRC 10
## GO:0031929 AKT1S1/SRC/TSC1/GSK3A/GATA3/ATM/VHL 7
## GO:0035051 MAPK1/TSC1/PDCD4/GSK3A/G6PD/EGFR/MYH11 7
## GO:2000641 SRC/MAPK1/MAP2K1/NF2 4
## GO:0038128 SRC/MAPK1/MAP2K1/EGFR 4
## ID Description GeneRatio BgRatio
## GO:0005925 GO:0005925 focal adhesion 7/34 421/19894
## GO:0030055 GO:0030055 cell-substrate junction 7/34 431/19894
## GO:0070522 GO:0070522 ERCC4-ERCC1 complex 2/34 4/19894
## GO:0000109 GO:0000109 nucleotide-excision repair complex 2/34 12/19894
## GO:0031256 GO:0031256 leading edge membrane 4/34 179/19894
## GO:0005901 GO:0005901 caveola 3/34 82/19894
## pvalue p.adjust qvalue
## GO:0005925 5.936393e-06 0.0005571557 0.0002804903
## GO:0030055 6.921189e-06 0.0005571557 0.0002804903
## GO:0070522 1.697422e-05 0.0009109496 0.0004586016
## GO:0000109 1.851213e-04 0.0074511307 0.0037511413
## GO:0031256 2.380182e-04 0.0076641868 0.0038584007
## GO:0005901 3.683101e-04 0.0098070624 0.0049371939
## geneID Count
## GO:0005925 SRC/MAPK1/VASP/ITGA2/YWHAE/MAP2K1/EGFR 7
## GO:0030055 SRC/MAPK1/VASP/ITGA2/YWHAE/MAP2K1/EGFR 7
## GO:0070522 XRCC1/ERCC1 2
## GO:0000109 XRCC1/ERCC1 2
## GO:0031256 SRC/VASP/EGFR/NF2 4
## GO:0005901 SRC/MAPK1/IRS1 3
## ID
## GO:0044389 GO:0044389
## GO:0030331 GO:0030331
## GO:0019887 GO:0019887
## GO:0016538 GO:0016538
## GO:0019207 GO:0019207
## GO:0045294 GO:0045294
## Description
## GO:0044389 ubiquitin-like protein ligase binding
## GO:0030331 nuclear estrogen receptor binding
## GO:0019887 protein kinase regulator activity
## GO:0016538 cyclin-dependent protein serine/threonine kinase regulator activity
## GO:0019207 kinase regulator activity
## GO:0045294 alpha-catenin binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0044389 6/34 324/18522 2.433845e-05 0.004948358 0.002443633
## GO:0030331 3/34 39/18522 4.936524e-05 0.004948358 0.002443633
## GO:0019887 5/34 232/18522 6.109083e-05 0.004948358 0.002443633
## GO:0016538 3/34 50/18522 1.044209e-04 0.005906158 0.002916621
## GO:0019207 5/34 270/18522 1.248624e-04 0.005906158 0.002916621
## GO:0045294 2/34 10/18522 1.458311e-04 0.005906158 0.002916621
## geneID Count
## GO:0044389 ERBB3/BECN1/CTNNB1/CCNB1/TUBA1B/PARP1 6
## GO:0030331 PCNA/CTNNB1/PARP1 3
## GO:0019887 ERBB3/CCNB1/CCNE2/RPTOR/CDKN2A 5
## GO:0016538 CCNB1/CCNE2/CDKN2A 3
## GO:0019207 ERBB3/CCNB1/CCNE2/RPTOR/CDKN2A 5
## GO:0045294 CDH2/CTNNB1 2
## ID Description GeneRatio
## GO:0009410 GO:0009410 response to xenobiotic stimulus 11/34
## GO:1901987 GO:1901987 regulation of cell cycle phase transition 11/34
## GO:0032200 GO:0032200 telomere organization 8/34
## GO:0000723 GO:0000723 telomere maintenance 7/34
## GO:0045786 GO:0045786 negative regulation of cell cycle 9/34
## GO:0044772 GO:0044772 mitotic cell cycle phase transition 9/34
## BgRatio pvalue p.adjust qvalue
## GO:0009410 444/18888 1.882340e-10 2.541885e-07 1.224154e-07
## GO:1901987 455/18888 2.440600e-10 2.541885e-07 1.224154e-07
## GO:0032200 189/18888 1.259232e-09 8.743266e-07 4.210694e-07
## GO:0000723 158/18888 1.116164e-08 5.812427e-06 2.799223e-06
## GO:0045786 405/18888 2.861415e-08 1.192066e-05 5.740903e-06
## GO:0044772 451/18888 7.192558e-08 2.497016e-05 1.202545e-05
## geneID
## GO:0009410 BECN1/ITGA2/PCNA/CTNNB1/ACACB/CDK1/E2F1/XRCC1/TYMS/ERRFI1/RPTOR
## GO:1901987 MAPK14/RAD51/BRCA2/ANLN/CDK1/E2F1/CCNB1/EZH2/CCNE2/RPTOR/CDKN2A
## GO:0032200 RAD51/BRCA2/PCNA/CTNNB1/XRCC1/EZH2/CCNE2/PARP1
## GO:0000723 RAD51/BRCA2/PCNA/CTNNB1/XRCC1/CCNE2/PARP1
## GO:0045786 MAPK14/RAD51/BRCA2/CTNNB1/CDK1/E2F1/CCNB1/EZH2/CDKN2A
## GO:0044772 ANLN/CDK1/E2F1/CCNB1/FOXM1/EZH2/CCNE2/RPTOR/CDKN2A
## Count
## GO:0009410 11
## GO:1901987 11
## GO:0032200 8
## GO:0000723 7
## GO:0045786 9
## GO:0044772 9
## ID Description
## GO:0000781 GO:0000781 chromosome, telomeric region
## GO:0098687 GO:0098687 chromosomal region
## GO:0000307 GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GO:0097125 GO:0097125 cyclin B1-CDK1 complex
## GO:1902554 GO:1902554 serine/threonine protein kinase complex
## GO:0005916 GO:0005916 fascia adherens
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0000781 7/34 173/19894 1.469642e-08 2.792320e-06 1.392293e-06
## GO:0098687 8/34 402/19894 2.972081e-07 2.823477e-05 1.407828e-05
## GO:0000307 4/34 56/19894 2.451862e-06 1.346679e-04 6.714743e-05
## GO:0097125 2/34 2/19894 2.835114e-06 1.346679e-04 6.714743e-05
## GO:1902554 4/34 136/19894 8.264048e-05 3.140338e-03 1.565820e-03
## GO:0005916 2/34 9/19894 1.013006e-04 3.207851e-03 1.599482e-03
## geneID Count
## GO:0000781 RAD51/BRCA2/PCNA/CDK1/XRCC1/EZH2/PARP1 7
## GO:0098687 RAD51/BRCA2/PCNA/CDK1/XRCC1/CCNB1/EZH2/PARP1 8
## GO:0000307 PCNA/CDK1/CCNB1/CCNE2 4
## GO:0097125 CDK1/CCNB1 2
## GO:1902554 PCNA/CDK1/CCNB1/CCNE2 4
## GO:0005916 CDH2/CTNNB1 2
## ID Description
## GO:0045309 GO:0045309 protein phosphorylated amino acid binding
## GO:0051219 GO:0051219 phosphoprotein binding
## GO:0043125 GO:0043125 ErbB-3 class receptor binding
## GO:0042169 GO:0042169 SH2 domain binding
## GO:0004715 GO:0004715 non-membrane spanning protein tyrosine kinase activity
## GO:0001784 GO:0001784 phosphotyrosine residue binding
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0045309 4/35 59/18522 4.515759e-06 0.0009257306 0.0005038637
## GO:0051219 4/35 93/18522 2.768030e-05 0.0023619941 0.0012856040
## GO:0043125 2/35 5/18522 3.456577e-05 0.0023619941 0.0012856040
## GO:0042169 3/35 42/18522 6.746261e-05 0.0032346697 0.0017605904
## GO:0004715 3/35 45/18522 8.306481e-05 0.0032346697 0.0017605904
## GO:0001784 3/35 47/18522 9.467326e-05 0.0032346697 0.0017605904
## geneID Count
## GO:0045309 MAPK1/LCK/YWHAB/SYK 4
## GO:0051219 MAPK1/LCK/YWHAB/SYK 4
## GO:0043125 ERBB3/NRG1 2
## GO:0042169 PTK2/LCK/SYK 3
## GO:0004715 PTK2/LCK/SYK 3
## GO:0001784 MAPK1/LCK/SYK 3
## ID Description
## GO:0051402 GO:0051402 neuron apoptotic process
## GO:0002757 GO:0002757 immune response-activating signaling pathway
## GO:0038133 GO:0038133 ERBB2-ERBB3 signaling pathway
## GO:0038129 GO:0038129 ERBB3 signaling pathway
## GO:0043254 GO:0043254 regulation of protein-containing complex assembly
## GO:0071383 GO:0071383 cellular response to steroid hormone stimulus
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0051402 8/36 292/18888 6.161328e-08 0.0001262456 0.0000676449
## GO:0002757 9/36 500/18888 2.959587e-07 0.0003032097 0.0001624658
## GO:0038133 3/36 9/18888 5.299354e-07 0.0003619459 0.0001939378
## GO:0038129 3/36 10/18888 7.560587e-07 0.0003872911 0.0002075182
## GO:0043254 8/36 418/18888 9.458263e-07 0.0003875996 0.0002076835
## GO:0071383 6/36 213/18888 2.814942e-06 0.0009613026 0.0005150850
## geneID Count
## GO:0051402 ERBB3/AKT2/GATA3/AXL/TP63/BID/PARP1/CASP9 8
## GO:0002757 ESR1/GATA3/MAPK1/BIRC2/PTK2/MS4A1/LCK/PARP1/SYK 9
## GO:0038133 ERBB3/MAPK1/NRG1 3
## GO:0038129 ERBB3/MAPK1/NRG1 3
## GO:0043254 CLDN7/EIF4G1/BIRC2/PRRT2/NRG1/BID/TFRC/SYK 8
## GO:0071383 ESR1/MAPK1/TP63/ERRFI1/PARP1/CASP9 6
## ID Description GeneRatio BgRatio pvalue
## GO:0031143 GO:0031143 pseudopodium 2/36 18/19894 0.0004783253
## GO:0005925 GO:0005925 focal adhesion 5/36 421/19894 0.0009099010
## GO:0030055 GO:0030055 cell-substrate junction 5/36 431/19894 0.0010105551
## GO:0044853 GO:0044853 plasma membrane raft 3/36 113/19894 0.0011114266
## GO:0016342 GO:0016342 catenin complex 2/36 31/19894 0.0014323951
## GO:0045121 GO:0045121 membrane raft 4/36 286/19894 0.0017151002
## p.adjust qvalue geneID Count
## GO:0031143 0.0429315 0.02638322 MAPK1/RAB25 2
## GO:0005925 0.0429315 0.02638322 MAPK1/PTK2/CTNNA1/MYH9/YWHAB 5
## GO:0030055 0.0429315 0.02638322 MAPK1/PTK2/CTNNA1/MYH9/YWHAB 5
## GO:0044853 0.0429315 0.02638322 MAPK1/MS4A1/CTNNA1 3
## GO:0016342 0.0429315 0.02638322 CDH3/CTNNA1 2
## GO:0045121 0.0429315 0.02638322 MAPK1/MS4A1/LCK/CTNNA1 4
## ID Description GeneRatio BgRatio
## GO:0045296 GO:0045296 cadherin binding 10/44 333/18522
## GO:0031625 GO:0031625 ubiquitin protein ligase binding 8/44 305/18522
## GO:0042826 GO:0042826 histone deacetylase binding 6/44 128/18522
## GO:0044389 GO:0044389 ubiquitin-like protein ligase binding 8/44 324/18522
## GO:0050815 GO:0050815 phosphoserine residue binding 3/44 10/18522
## GO:0008013 GO:0008013 beta-catenin binding 5/44 86/18522
## pvalue p.adjust qvalue
## GO:0045296 4.449265e-09 1.299185e-06 6.509977e-07
## GO:0031625 5.222688e-07 5.364286e-05 2.687944e-05
## GO:0042826 5.511253e-07 5.364286e-05 2.687944e-05
## GO:0044389 8.238420e-07 6.014046e-05 3.013527e-05
## GO:0050815 1.483568e-06 8.664034e-05 4.341387e-05
## GO:0008013 1.806890e-06 8.793532e-05 4.406276e-05
## geneID Count
## GO:0045296 CDH1/YWHAZ/YWHAE/NDRG1/FASN/MYH9/CTNNA1/EEF2/PRDX1/YWHAB 10
## GO:0031625 TUBA1B/YWHAZ/YWHAE/TP53/CDKN1A/CDKN1B/PARP1/GSK3B 8
## GO:0042826 MAPK8/YWHAE/TP53/CCND1/PARP1/YWHAB 6
## GO:0044389 TUBA1B/YWHAZ/YWHAE/TP53/CDKN1A/CDKN1B/PARP1/GSK3B 8
## GO:0050815 YWHAZ/YWHAE/YWHAB 3
## GO:0008013 CDH1/AR/CTNNA1/GSK3B/PXN 5
## ID
## GO:0034504 GO:0034504
## GO:1900180 GO:1900180
## GO:0031334 GO:0031334
## GO:0045936 GO:0045936
## GO:0010563 GO:0010563
## GO:0062197 GO:0062197
## Description GeneRatio
## GO:0034504 protein localization to nucleus 12/44
## GO:1900180 regulation of protein localization to nucleus 9/44
## GO:0031334 positive regulation of protein-containing complex assembly 9/44
## GO:0045936 negative regulation of phosphate metabolic process 11/44
## GO:0010563 negative regulation of phosphorus metabolic process 11/44
## GO:0062197 cellular response to chemical stress 10/44
## BgRatio pvalue p.adjust qvalue
## GO:0034504 311/18888 4.232578e-12 1.086079e-08 5.243941e-09
## GO:1900180 144/18888 3.820625e-11 4.901862e-08 2.366777e-08
## GO:0031334 197/18888 6.290483e-10 3.995743e-07 1.929273e-07
## GO:0045936 378/18888 7.572262e-10 3.995743e-07 1.929273e-07
## GO:0010563 379/18888 7.785937e-10 3.995743e-07 1.929273e-07
## GO:0062197 311/18888 1.917069e-09 8.198664e-07 3.958579e-07
## geneID
## GO:0034504 CDH1/YWHAZ/YWHAE/TP53/CDKN1A/NF2/PARP1/CTNNA1/MTOR/GSK3B/TFRC/WWTR1
## GO:1900180 CDH1/YWHAZ/NF2/PARP1/CTNNA1/MTOR/GSK3B/TFRC/WWTR1
## GO:0031334 ATM/MAPK8/EIF4G1/TP53/CDKN1B/BCL2L11/MTOR/GSK3B/TFRC
## GO:0045936 EIF4G1/YWHAE/TP53/CDKN1A/NF2/ADAR/CDKN1B/PARP1/GSK3B/WWTR1/YWHAB
## GO:0010563 EIF4G1/YWHAE/TP53/CDKN1A/NF2/ADAR/CDKN1B/PARP1/GSK3B/WWTR1/YWHAB
## GO:0062197 CASP3/ATM/MAPK8/TP53/MAPK1/PARP1/MTOR/PRDX1/PRKAA1/PXN
## Count
## GO:0034504 12
## GO:1900180 9
## GO:0031334 9
## GO:0045936 11
## GO:0010563 11
## GO:0062197 10
## ID Description GeneRatio BgRatio pvalue
## GO:0042470 GO:0042470 melanosome 6/44 112/19894 1.649743e-07
## GO:0048770 GO:0048770 pigment granule 6/44 112/19894 1.649743e-07
## GO:0005901 GO:0005901 caveola 4/44 82/19894 3.210058e-05
## GO:0005925 GO:0005925 focal adhesion 7/44 421/19894 3.524035e-05
## GO:0030055 GO:0030055 cell-substrate junction 7/44 431/19894 4.090619e-05
## GO:0005912 GO:0005912 adherens junction 5/44 188/19894 5.754759e-05
## p.adjust qvalue geneID
## GO:0042470 1.657992e-05 1.024577e-05 YWHAZ/YWHAE/FASN/PRDX1/TFRC/YWHAB
## GO:0048770 1.657992e-05 1.024577e-05 YWHAZ/YWHAE/FASN/PRDX1/TFRC/YWHAB
## GO:0005901 1.644429e-03 1.016196e-03 CDH1/MAPK1/CTNNA1/IGF1R
## GO:0005925 1.644429e-03 1.016196e-03 YWHAZ/YWHAE/MAPK1/MYH9/CTNNA1/PXN/YWHAB
## GO:0030055 1.644429e-03 1.016196e-03 YWHAZ/YWHAE/MAPK1/MYH9/CTNNA1/PXN/YWHAB
## GO:0005912 1.927844e-03 1.191336e-03 CDH1/NDRG1/NF2/MYH9/CTNNA1
## Count
## GO:0042470 6
## GO:0048770 6
## GO:0005901 4
## GO:0005925 7
## GO:0030055 7
## GO:0005912 5
## ID Description GeneRatio
## GO:0004674 GO:0004674 protein serine/threonine kinase activity 15/71
## GO:0106310 GO:0106310 protein serine kinase activity 14/71
## GO:0019902 GO:0019902 phosphatase binding 10/71
## GO:0019903 GO:0019903 protein phosphatase binding 9/71
## GO:0043548 GO:0043548 phosphatidylinositol 3-kinase binding 5/71
## GO:0019207 GO:0019207 kinase regulator activity 10/71
## BgRatio pvalue p.adjust qvalue
## GO:0004674 427/18522 6.087015e-11 1.679792e-08 7.710955e-09
## GO:0106310 363/18522 8.420009e-11 1.679792e-08 7.710955e-09
## GO:0019902 189/18522 2.595931e-09 3.452588e-07 1.584884e-07
## GO:0019903 142/18522 3.526298e-09 3.517482e-07 1.614673e-07
## GO:0043548 25/18522 3.590014e-08 2.864831e-06 1.315079e-06
## GO:0019207 270/18522 7.747783e-08 5.152276e-06 2.365113e-06
## geneID
## GO:0004674 CDK1/RPS6KB1/MAPK14/EGFR/ARAF/MAPK9/AKT2/MAP2K1/AKT3/GSK3B/PRKAA1/PRKCA/MAPK3/MAPK8/BRAF
## GO:0106310 CDK1/RPS6KB1/MAPK14/ARAF/MAPK9/AKT2/MAP2K1/AKT3/GSK3B/PRKAA1/PRKCA/MAPK3/MAPK8/BRAF
## GO:0019902 PIK3R1/RPS6KB1/MAPK14/EGFR/PIK3R2/TP53/CTNNB1/MAPK3/MAPK8/PXN
## GO:0019903 PIK3R1/RPS6KB1/MAPK14/EGFR/PIK3R2/TP53/CTNNB1/MAPK8/PXN
## GO:0043548 PIK3R1/IRS1/PIK3R2/IGF1R/BECN1
## GO:0019207 CCNE1/CAV1/PIK3R1/CCND1/CDKN1A/EGFR/PIK3R2/MAP2K1/CCNB1/YWHAB
## Count
## GO:0004674 15
## GO:0106310 14
## GO:0019902 10
## GO:0019903 9
## GO:0043548 5
## GO:0019207 10
## ID Description GeneRatio
## GO:0018105 GO:0018105 peptidyl-serine phosphorylation 18/72
## GO:0018209 GO:0018209 peptidyl-serine modification 18/72
## GO:0048732 GO:0048732 gland development 20/72
## GO:0071214 GO:0071214 cellular response to abiotic stimulus 18/72
## GO:0104004 GO:0104004 cellular response to environmental stimulus 18/72
## GO:0009410 GO:0009410 response to xenobiotic stimulus 19/72
## BgRatio pvalue p.adjust qvalue
## GO:0018105 282/18888 1.586060e-17 5.592449e-14 2.502636e-14
## GO:0018209 294/18888 3.325078e-17 5.862112e-14 2.623311e-14
## GO:0048732 449/18888 2.182362e-16 2.226695e-13 9.964523e-14
## GO:0071214 334/18888 3.157537e-16 2.226695e-13 9.964523e-14
## GO:0104004 334/18888 3.157537e-16 2.226695e-13 9.964523e-14
## GO:0009410 444/18888 2.885601e-15 1.695771e-12 7.588623e-13
## geneID
## GO:0018105 PTEN/CAV1/CDK1/RPS6KB1/MAPK14/EGFR/ARAF/MAPK9/PTGS2/AKT2/AKT3/EIF4G1/GSK3B/PRKAA1/PRKCA/MAPK8/TFRC/BRAF
## GO:0018209 PTEN/CAV1/CDK1/RPS6KB1/MAPK14/EGFR/ARAF/MAPK9/PTGS2/AKT2/AKT3/EIF4G1/GSK3B/PRKAA1/PRKCA/MAPK8/TFRC/BRAF
## GO:0048732 CAV1/ITGA2/SRSF1/CCND1/EGFR/TP63/EZH2/BRCA2/TYMS/AKT2/MAP2K1/NFKB1/ERRFI1/CTNNB1/SMAD4/PCNA/MAPK3/TGM2/FASN/BRAF
## GO:0071214 PTEN/PIK3R1/ITGA2/RAD51/MAPK14/CDKN1A/MYC/EGFR/BRCA2/PTGS2/TP53/AKT2/NFKB1/IGF1R/PCNA/MAPK3/MAPK8/RAB11B
## GO:0104004 PTEN/PIK3R1/ITGA2/RAD51/MAPK14/CDKN1A/MYC/EGFR/BRCA2/PTGS2/TP53/AKT2/NFKB1/IGF1R/PCNA/MAPK3/MAPK8/RAB11B
## GO:0009410 CDK1/ITGA2/RPS6KB1/E2F1/CCND1/CDKN1A/MYC/EGFR/PTGS2/TYMS/TP53/ERRFI1/CTNNB1/IGFBP2/PCNA/PRKAA1/TFRC/BECN1/BRAF
## Count
## GO:0018105 18
## GO:0018209 18
## GO:0048732 20
## GO:0071214 18
## GO:0104004 18
## GO:0009410 19
## ID
## GO:0061695 GO:0061695
## GO:1902911 GO:1902911
## GO:0005901 GO:0005901
## GO:0005925 GO:0005925
## GO:0030055 GO:0030055
## GO:0000307 GO:0000307
## Description
## GO:0061695 transferase complex, transferring phosphorus-containing groups
## GO:1902911 protein kinase complex
## GO:0005901 caveola
## GO:0005925 focal adhesion
## GO:0030055 cell-substrate junction
## GO:0000307 cyclin-dependent protein kinase holoenzyme complex
## GeneRatio BgRatio pvalue p.adjust qvalue
## GO:0061695 12/72 308/19894 1.026747e-09 3.172649e-07 1.653604e-07
## GO:1902911 9/72 150/19894 3.513936e-09 5.429032e-07 2.829643e-07
## GO:0005901 7/72 82/19894 1.848300e-08 1.903749e-06 9.922452e-07
## GO:0005925 12/72 421/19894 3.368808e-08 2.602404e-06 1.356389e-06
## GO:0030055 12/72 431/19894 4.356805e-08 2.633625e-06 1.372661e-06
## GO:0000307 6/72 56/19894 5.113836e-08 2.633625e-06 1.372661e-06
## geneID
## GO:0061695 CCNE1/PIK3R1/CDK1/CCND1/CDKN1A/IRS1/PIK3R2/CCNB1/IGF1R/PCNA/PRKAA1/BECN1
## GO:1902911 CCNE1/CDK1/CCND1/CDKN1A/IRS1/CCNB1/IGF1R/PCNA/PRKAA1
## GO:0005901 CAV1/IRS1/PTGS2/CTNNA1/CTNNB1/IGF1R/MAPK3
## GO:0005925 CAV1/ITGA2/MYH9/EGFR/PIK3R2/MAP2K1/CTNNA1/CTNNB1/MAPK3/PXN/TGM2/YWHAB
## GO:0030055 CAV1/ITGA2/MYH9/EGFR/PIK3R2/MAP2K1/CTNNA1/CTNNB1/MAPK3/PXN/TGM2/YWHAB
## GO:0000307 CCNE1/CDK1/CCND1/CDKN1A/CCNB1/PCNA
## Count
## GO:0061695 12
## GO:1902911 9
## GO:0005901 7
## GO:0005925 12
## GO:0030055 12
## GO:0000307 6barplot(ego_MF[[1]], title = "enrichGO, Molecular Function, Factor 1 of 1")
barplot(ego_MF[[2]], title = "enrichGO, Molecular Function, Factor 1 of 2")
barplot(ego_MF[[3]], title = "enrichGO, Molecular Function, Factor 2 of 2")
barplot(ego_MF[[4]], title = "enrichGO, Molecular Function, Factor 1 of 3")
barplot(ego_MF[[5]], title = "enrichGO, Molecular Function, Factor 2 of 3")
barplot(ego_MF[[6]], title = "enrichGO, Molecular Function, Factor 3 of 3")
barplot(ego_MF[[7]], title = "enrichGO, Molecular Function, Factor 1 of 5")
barplot(ego_MF[[8]], title = "enrichGO, Molecular Function, Factor 2 of 5")
barplot(ego_MF[[9]], title = "enrichGO, Molecular Function, Factor 3 of 5")
barplot(ego_MF[[10]], title = "enrichGO, Molecular Function, Factor 4 of 5")
barplot(ego_MF[[11]], title = "enrichGO, Molecular Function, Factor 5 of 5")
barplot(ego_MF[[12]], title = "enrichGO, Molecular Function, Factor 1 of 10")
barplot(ego_MF[[13]], title = "enrichGO, Molecular Function, Factor 2 of 10")
barplot(ego_MF[[14]], title = "enrichGO, Molecular Function, Factor 3 of 10")
barplot(ego_MF[[15]], title = "enrichGO, Molecular Function, Factor 4 of 10")
barplot(ego_MF[[16]], title = "enrichGO, Molecular Function, Factor 5 of 10")
barplot(ego_MF[[17]], title = "enrichGO, Molecular Function, Factor 6 of 10")
barplot(ego_MF[[18]], title = "enrichGO, Molecular Function, Factor 7 of 10")
barplot(ego_MF[[19]], title = "enrichGO, Molecular Function, Factor 8 of 10")
barplot(ego_MF[[20]], title = "enrichGO, Molecular Function, Factor 9 of 10")
barplot(ego_MF[[21]], title = "enrichGO, Molecular Function, Factor 10 of 10")
barplot(ego_BP[[1]], title = "enrichGO, Biological Process, Factor 1 of 1")
barplot(ego_BP[[2]], title = "enrichGO, Biological Process, Factor 1 of 2")
barplot(ego_BP[[3]], title = "enrichGO, Biological Process, Factor 2 of 2")
barplot(ego_BP[[4]], title = "enrichGO, Biological Process, Factor 1 of 3")
barplot(ego_BP[[5]], title = "enrichGO, Biological Process, Factor 2 of 3")
barplot(ego_BP[[6]], title = "enrichGO, Biological Process, Factor 3 of 3")
barplot(ego_BP[[7]], title = "enrichGO, Biological Process, Factor 1 of 5")
barplot(ego_BP[[8]], title = "enrichGO, Biological Process, Factor 2 of 5")
barplot(ego_BP[[9]], title = "enrichGO, Biological Process, Factor 3 of 5")
barplot(ego_BP[[10]], title = "enrichGO, Biological Process, Factor 4 of 5")
barplot(ego_BP[[11]], title = "enrichGO, Biological Process, Factor 5 of 5")
barplot(ego_BP[[12]], title = "enrichGO, Biological Process, Factor 1 of 10")
barplot(ego_BP[[13]], title = "enrichGO, Biological Process, Factor 2 of 10")
barplot(ego_BP[[14]], title = "enrichGO, Biological Process, Factor 3 of 10")
barplot(ego_BP[[15]], title = "enrichGO, Biological Process, Factor 4 of 10")
barplot(ego_BP[[16]], title = "enrichGO, Biological Process, Factor 5 of 10")
barplot(ego_BP[[17]], title = "enrichGO, Biological Process, Factor 6 of 10")
barplot(ego_BP[[18]], title = "enrichGO, Biological Process, Factor 7 of 10")
barplot(ego_BP[[19]], title = "enrichGO, Biological Process, Factor 8 of 10")
barplot(ego_BP[[20]], title = "enrichGO, Biological Process, Factor 9 of 10")
barplot(ego_BP[[21]], title = "enrichGO, Biological Process, Factor 10 of 10")
barplot(ego_CC[[1]], title = "enrichGO, Cellular Component, Factor 1 of 1")
barplot(ego_CC[[2]], title = "enrichGO, Cellular Component, Factor 1 of 2")
barplot(ego_CC[[3]], title = "enrichGO, Cellular Component, Factor 2 of 2")
barplot(ego_CC[[4]], title = "enrichGO, Cellular Component, Factor 1 of 3")
barplot(ego_CC[[5]], title = "enrichGO, Cellular Component, Factor 2 of 3")
barplot(ego_CC[[6]], title = "enrichGO, Cellular Component, Factor 3 of 3")
barplot(ego_CC[[7]], title = "enrichGO, Cellular Component, Factor 1 of 5")
barplot(ego_CC[[8]], title = "enrichGO, Cellular Component, Factor 2 of 5")
barplot(ego_CC[[9]], title = "enrichGO, Cellular Component, Factor 3 of 5")
barplot(ego_CC[[10]], title = "enrichGO, Cellular Component, Factor 4 of 5")
barplot(ego_CC[[11]], title = "enrichGO, Cellular Component, Factor 5 of 5")
barplot(ego_CC[[12]], title = "enrichGO, Cellular Component, Factor 1 of 10")
barplot(ego_CC[[13]], title = "enrichGO, Cellular Component, Factor 2 of 10")
barplot(ego_CC[[14]], title = "enrichGO, Cellular Component, Factor 3 of 10")
barplot(ego_CC[[15]], title = "enrichGO, Cellular Component, Factor 4 of 10")
barplot(ego_CC[[16]], title = "enrichGO, Cellular Component, Factor 5 of 10")
barplot(ego_CC[[17]], title = "enrichGO, Cellular Component, Factor 6 of 10")
barplot(ego_CC[[18]], title = "enrichGO, Cellular Component, Factor 7 of 10")
barplot(ego_CC[[19]], title = "enrichGO, Cellular Component, Factor 8 of 10")
barplot(ego_CC[[20]], title = "enrichGO, Cellular Component, Factor 9 of 10")
barplot(ego_CC[[21]], title = "enrichGO, Cellular Component, Factor 10 of 10")
DAG plots for ego
goplot(ego_MF[[1]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 1")
goplot(ego_MF[[2]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 2")
goplot(ego_MF[[3]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 2")
goplot(ego_MF[[4]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 3")
goplot(ego_MF[[5]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 3")
goplot(ego_MF[[6]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 3")
goplot(ego_MF[[7]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 5")
goplot(ego_MF[[8]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 5")
goplot(ego_MF[[9]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 5")
goplot(ego_MF[[10]]) + labs(title = "enrichGO, Molecular Function, Factor 4 of 5")
goplot(ego_MF[[11]]) + labs(title = "enrichGO, Molecular Function, Factor 5 of 5")
goplot(ego_MF[[12]]) + labs(title = "enrichGO, Molecular Function, Factor 1 of 10")
goplot(ego_MF[[13]]) + labs(title = "enrichGO, Molecular Function, Factor 2 of 10")
goplot(ego_MF[[14]]) + labs(title = "enrichGO, Molecular Function, Factor 3 of 10")
goplot(ego_MF[[15]]) + labs(title = "enrichGO, Molecular Function, Factor 4 of 10")
goplot(ego_MF[[16]]) + labs(title = "enrichGO, Molecular Function, Factor 5 of 10")
goplot(ego_MF[[17]]) + labs(title = "enrichGO, Molecular Function, Factor 6 of 10")
goplot(ego_MF[[18]]) + labs(title = "enrichGO, Molecular Function, Factor 7 of 10")
goplot(ego_MF[[19]]) + labs(title = "enrichGO, Molecular Function, Factor 8 of 10")
goplot(ego_MF[[20]]) + labs(title = "enrichGO, Molecular Function, Factor 9 of 10")
goplot(ego_MF[[21]]) + labs(title = "enrichGO, Molecular Function, Factor 10 of 10")
goplot(ego_BP[[1]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 1")
goplot(ego_BP[[2]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 2")## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[3]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 2")
goplot(ego_BP[[4]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 3")
goplot(ego_BP[[5]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 3")
goplot(ego_BP[[6]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 3")## Warning: ggrepel: 6 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[7]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 5")
goplot(ego_BP[[8]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 5")
goplot(ego_BP[[9]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 5")
goplot(ego_BP[[10]]) + labs(title = "enrichGO, Biological Process, Factor 4 of 5")
goplot(ego_BP[[11]]) + labs(title = "enrichGO, Biological Process, Factor 5 of 5")
goplot(ego_BP[[12]]) + labs(title = "enrichGO, Biological Process, Factor 1 of 10")## Warning: ggrepel: 2 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[13]]) + labs(title = "enrichGO, Biological Process, Factor 2 of 10")
goplot(ego_BP[[14]]) + labs(title = "enrichGO, Biological Process, Factor 3 of 10")## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[15]]) + labs(title = "enrichGO, Biological Process, Factor 4 of 10")
goplot(ego_BP[[16]]) + labs(title = "enrichGO, Biological Process, Factor 5 of 10")## Warning: ggrepel: 5 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[17]]) + labs(title = "enrichGO, Biological Process, Factor 6 of 10")## Warning: ggrepel: 10 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[18]]) + labs(title = "enrichGO, Biological Process, Factor 7 of 10")## Warning: ggrepel: 4 unlabeled data points (too many overlaps). Consider
## increasing max.overlaps
goplot(ego_BP[[19]]) + labs(title = "enrichGO, Biological Process, Factor 8 of 10")
goplot(ego_BP[[20]]) + labs(title = "enrichGO, Biological Process, Factor 9 of 10")
goplot(ego_BP[[21]]) + labs(title = "enrichGO, Biological Process, Factor 10 of 10")
goplot(ego_CC[[1]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 1")
goplot(ego_CC[[2]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 2")
goplot(ego_CC[[3]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 2")
goplot(ego_CC[[4]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 3")
goplot(ego_CC[[5]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 3")
goplot(ego_CC[[6]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 3")
goplot(ego_CC[[7]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 5")
goplot(ego_CC[[8]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 5")
goplot(ego_CC[[9]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 5")
goplot(ego_CC[[10]]) + labs(title = "enrichGO, Cellular Component, Factor 4 of 5")
goplot(ego_CC[[11]]) + labs(title = "enrichGO, Cellular Component, Factor 5 of 5")
goplot(ego_CC[[12]]) + labs(title = "enrichGO, Cellular Component, Factor 1 of 10")
goplot(ego_CC[[13]]) + labs(title = "enrichGO, Cellular Component, Factor 2 of 10")
goplot(ego_CC[[14]]) + labs(title = "enrichGO, Cellular Component, Factor 3 of 10")
goplot(ego_CC[[15]]) + labs(title = "enrichGO, Cellular Component, Factor 4 of 10")
goplot(ego_CC[[16]]) + labs(title = "enrichGO, Cellular Component, Factor 5 of 10")
goplot(ego_CC[[17]]) + labs(title = "enrichGO, Cellular Component, Factor 6 of 10")
goplot(ego_CC[[18]]) + labs(title = "enrichGO, Cellular Component, Factor 7 of 10")
goplot(ego_CC[[19]]) + labs(title = "enrichGO, Cellular Component, Factor 8 of 10")
goplot(ego_CC[[20]]) + labs(title = "enrichGO, Cellular Component, Factor 9 of 10")
goplot(ego_CC[[21]]) + labs(title = "enrichGO, Cellular Component, Factor 10 of 10")
3. Export Pathway Analysis result to data
pathway = list("ggo_MF" = ggo_MF,
"ggo_BP" = ggo_BP,
"ggo_CC" = ggo_CC,
"ego_MF" = ego_MF,
"ego_BP" = ego_BP,
"ego_CC" = ego_CC)
saveRDS(pathway, file = "data/out_pathway/pathways_mofa_top_5_percent.rds")